{"id":1344,"date":"2014-10-21T17:31:03","date_gmt":"2014-10-21T15:31:03","guid":{"rendered":"http:\/\/www.h-its.org\/?page_id=1344"},"modified":"2020-04-02T12:17:20","modified_gmt":"2020-04-02T10:17:20","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.h-its.org\/de\/forschung\/mcm\/publications\/","title":{"rendered":"Publikationen"},"content":{"rendered":"\n  <div class=\"hits-blocks hits-publications-block\">\n\n      <div class=\"hits-tabs\">\n        <nav>\n          <ul>\n                          <li class=\"is-active\"><a href=\"#\" >Publikationen<\/a><\/li>\n                                      <li class=\"is-active\"><a href=\"#\" >Abschlussarbeiten<\/a><\/li>\n                                      <li class=\"is-active\"><a href=\"#\" >Patente<\/a><\/li>\n                      <\/ul>\n        <\/nav>\n        <div class=\"content\">\n                      <div class=\"hits-tabs--tab\">\n            \n              <\/ul><h2 id=\"publication-year-2026\">2026<\/h2><ul class=\"publications-list\"><li>Milanesi M, Urbinati C, Zimmermann L, Oreste P, Zani A, Caruso A, Caccuri F, Laketa V, Chlanda P, Wade RC, Rusnati M, Paiardi G (2026). <a href=\"https:\/\/doi.org\/10.1038\/s44298-025-00163-4\"><span class=\"publication-title\">K5 polysaccharides inhibit SARS-CoV-2 infection by preventing spike-proteolytic priming<\/span><\/a>, npj Viruses 4(1):3. <span style=\"color:#ddd; font-size:12px\">2220<\/span><\/li><\/ul><h2 id=\"publication-year-2025\">2025<\/h2><ul class=\"publications-list\"><li>Sch\u00fctt I, Einwohlt P, Wandinger A, Teuffel J, Wirsing R, Hlawatschke BH, Fehlauer HL, Bothe S, Bader N, Monaci E, Kreikemeyer B, Schindelin H, Wade RC, Fiedler T (2025). <a href=\"https:\/\/doi.org\/10.1080\/21505594.2025.2609393\"><span class=\"publication-title\">Inhibitors of GapN-dependent NADPH supply as potential lead compounds for novel therapeutics against\r\n                    <i>Streptococcus pyogenes<\/i><\/span><\/a>, Virulence 17(1):2609393. <span style=\"color:#ddd; font-size:12px\">2132<\/span><\/li><li>Mu\u00f1iz-Chicharro A, Ganotra GK, Wade RC (2025). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.5c01488\"><span class=\"publication-title\">A Multiscale Simulation Approach to Compute Protein\u2013Ligand Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics<\/span><\/a>, J. Chem. Inf. Model. 65(20):11215-11231. <span style=\"color:#ddd; font-size:12px\">2092<\/span><\/li><li>Panecka-Hofman J, Linciano P, P\u00f6hner I, Dyguda-Kazimierowicz E, Jedwabny W, Landi G, Santarem N, Witt G, Ellinger B, Kuzikov M, Luciani R, Ferrari S, Aiello D, Mangani S, Pozzi C, Cordeiro-da-Silva A, Gul S, Costi MP, Wade RC (2025). <a href=\"https:\/\/doi.org\/10.1021\/acs.jmedchem.5c01799\"><span class=\"publication-title\">Design of 2-Aminobenzothiazole Derivatives Targeting Trypanosomatid PTR1 by a Multidisciplinary Fragment Hybridization Approach<\/span><\/a>, J. Med. Chem. 68(19):20595-20618. <span style=\"color:#ddd; font-size:12px\">2093<\/span><\/li><li>Reinhardt M, Bruce NJ, Kokh DB, Wade RC (2025). <a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.5c01046\"><span class=\"publication-title\">Correction to \u201cBrownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics\u201d<\/span><\/a>, J. Chem. Theory Comput. 21(15):7724-7725. <span style=\"color:#ddd; font-size:12px\">2071<\/span><\/li><li>Teuffel J, Mukherjee G, Han SB, Elstner M, Wade RC (2025). <a href=\"https:\/\/doi.org\/10.1063\/5.0248701\"><span class=\"publication-title\">On the determinants of electron transfer reorganization energy in a cytochrome P450: cytochrome b5 complex. A combined quantum mechanics and molecular dynamics simulation study<\/span><\/a>, The Journal of Chemical Physics 162(19):195101. <span style=\"color:#ddd; font-size:12px\">2064<\/span><\/li><li>Athanasiou C, Cabezudo AC, Tsengenes A, Wade RC (2025). <a href=\"https:\/\/doi.org\/10.1021\/jacsau.5c00174\"><span class=\"publication-title\">Simulation of Neurotrophin Receptor Transmembrane Helix Interactions Reveals Active States and Distinct Signaling Mechanisms<\/span><\/a>, JACS Au 5(5):2186-2200. <span style=\"color:#ddd; font-size:12px\">2063<\/span><\/li><li>Ferraz MV, Adan WCS, Lima TE, Santos AJ, Paula SOd, Dhalia R, Wallau GL, Wade RC, Viana IF, Lins RD (2025). <a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1012921\"><span class=\"publication-title\">Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning<\/span><\/a>, PLoS Comput Biol 21(4):e1012921. <span style=\"color:#ddd; font-size:12px\">2062<\/span><\/li><li>Amaro RE, Aqvist J, Bahar I, Battistini F, Bellaiche A, Beltran D, Biggin PC, Bonomi M, Bowman GR, Bryce RA, Bussi G, Carloni P, Case DA, Cavalli A, Chang CA, Cheatham TE3, Cheung MS, Chipot C, Chong LT, Choudhary P, Cisneros GA, Clementi C, Collepardo-Guevara R, Coveney P, Covino R, Crawford TD, Peraro MD, Groot BLd, Delemotte L, Vivo MD, Essex JW, Fraternali F, Gao J, Gelpi JL, Gervasio FL, Gonzalez-Nilo FD, Grubmuller H, Guenza MG, Guzman HV, Harris S, Head-Gordon T, Hernandez R, Hospital A, Huang N, Huang X, Hummer G, Iglesias-Fernandez J, Jensen JH, Jha S, Jiao W, Jorgensen WL, Kamerlin SCL, Khalid S, Laughton C, Levitt M, Limongelli V, Lindahl E, Lindorff-Larsen K, Loverde S, Lundborg M, Luo YL, Luque FJ, Lynch CI, MacKerell ADJ, Magistrato A, Marrink SJ, Martin H, McCammon JA, Merz K, Moliner V, Mulholland AJ, Murad S, Naganathan AN, Nangia S, Noe F, Noy A, Olah J, O&#8217;Mara ML, Ondrechen MJ, Onuchic JN, Onufriev A, Osuna S, Palermo G, Panchenko AR, Pantano S, Parish C, Parrinello M, Perez A, Perez-Acle T, Perilla JR, Pettitt BM, Pietropaolo A, Piquemal JP, Poma AB, Praprotnik M, Ramos MJ, Ren P, Reuter N, Roitberg A, Rosta E, Rovira C, Roux B, Rothlisberger U, Sanbonmatsu KY, Schlick T, Shaytan AK, Simmerling C, Smith JC, Sugita Y, Swiderek K, Taiji M, Tao P, Tieleman DP, Tikhonova IG, Tirado-Rives J, Tunon I, Kamp MWvd, Spoel Dvd, Velankar S, Voth GA, Wade R, Warshel A, Welborn VV, Wetmore SD, Wheeler TJ, Wong CF, Yang LW, Zacharias M, Orozco M (2025). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/40175561\"><span class=\"publication-title\">The need to implement FAIR principles in biomolecular simulations.<\/span><\/a>, Nat Methods. 2025 Apr;22(4):641-645. doi: 10.1038\/s41592-025-02635-0. <span style=\"color:#ddd; font-size:12px\">2049<\/span><\/li><li>Kehr D, Ritterhoff J, Glaser M, Jarosch L, Salazar RE, Spaich K, Varadi K, Birkenstock J, Egger M, Gao E, Koch WJ, Sauter M, Freichel M, Katus HA, Frey N, Jungmann A, Busch C, Mather PJ, Ruhparwar A, Busch M, V\u00f6lkers M, Wade RC, Most P (2025). <a href=\"https:\/\/doi.org\/10.1161\/circulationaha.123.066961\"><span class=\"publication-title\">S100A1ct: A Synthetic Peptide Derived From S100A1 Protein Improves Cardiac Performance and Survival in Preclinical Heart Failure Models<\/span><\/a>, Circulation 151(8):548-565. <span style=\"color:#ddd; font-size:12px\">2016<\/span><\/li><\/ul><h2 id=\"publication-year-2024\">2024<\/h2><ul class=\"publications-list\"><li>Guerra J, Belleri M, Paiardi G, Tobia C, Capoferri D, Corli M, Scalvini E, Ghirimoldi M, Manfredi M, Wade RC, Presta M, Mignani L (2024). <a href=\"https:\/\/doi.org\/10.1016\/j.csbj.2024.03.023\"><span class=\"publication-title\">Impact of an irreversible \u03b2-galactosylceramidase inhibitor on the lipid profile of zebrafish embryos<\/span><\/a>, Computational and Structural Biotechnology Journal 23:1397-1407. <span style=\"color:#ddd; font-size:12px\">1839<\/span><\/li><li>Paiardi G, Ferraz M, Rusnati M, Wade RC (2024). <a href=\"https:\/\/doi.org\/10.1073\/pnas.2404892121\"><span class=\"publication-title\">The accomplices: Heparan sulfates and N-glycans foster SARS-CoV-2 spike:ACE2 receptor binding and virus priming<\/span><\/a>, Proc. Natl. Acad. Sci. U.S.A. 121(43):e2404892121. <span style=\"color:#ddd; font-size:12px\">1872<\/span><\/li><li>Han SB, Teuffel J, Mukherjee G, Wade RC (2024). <a href=\"https:\/\/doi.org\/10.1002\/pro.5165\"><span class=\"publication-title\">Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane\u2010bound cytochrome P450 2B4<\/span><\/a>, Protein Science 33(10):e5165. <span style=\"color:#ddd; font-size:12px\">1870<\/span><\/li><li>D\u2019Arrigo G, Kokh DB, Nunes-Alves A, Wade RC (2024). <a href=\"https:\/\/doi.org\/10.1038\/s42003-024-06880-5\"><span class=\"publication-title\">Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by \u03c4RAMD<\/span><\/a>, Commun Biol 7(1):1159. <span style=\"color:#ddd; font-size:12px\">1880<\/span><\/li><li>Gryn\u2019ova G, Bereau T, M\u00fcller C, Friederich P, Wade RC, Nunes-Alves A, Soares TA, Merz K (2024). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.4c01300\"><span class=\"publication-title\">EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning<\/span><\/a>, J. Chem. Inf. Model. 64(15):5737-5738. <span style=\"color:#ddd; font-size:12px\">1855<\/span><\/li><li>Charou D, Rogdakis T, Latorrata A, Valcarcel M, Papadogiannis V, Athanasiou C, Tsengenes A, Papadopoulou MA, Lypitkas D, Lavigne MD, Katsila T, Wade RC, Cader MZ, Calogeropoulou T, Gravanis A, Charalampopoulos I (2024). <a href=\"https:\/\/doi.org\/10.1186\/s13287-024-03818-w\"><span class=\"publication-title\">Comprehensive characterization of the neurogenic and neuroprotective action of a novel TrkB agonist using mouse and human stem cell models of Alzheimer\u2019s disease<\/span><\/a>, Stem Cell Res Ther 15(1):200. <span style=\"color:#ddd; font-size:12px\">1886<\/span><\/li><li>Weidner P, Saar D, S\u00f6hn M, Schroeder T, Yu Y, Z\u00f6llner FG, Ponelies N, Zhou X, Zwicky A, Rohrbacher FN, Pattabiraman VR, Tanriver M, Bauer A, Ahmed H, Ametamey SM, Riffel P, Seger R, Bode JW, Wade RC, Ebert MP, Kragelund BB, Burgermeister E (2024). <a href=\"https:\/\/doi.org\/10.1016\/j.canlet.2024.216783\"><span class=\"publication-title\">Myotubularin-related-protein-7 inhibits mutant (G12V) K-RAS by direct interaction<\/span><\/a>, Cancer Letters 588:216783. <span style=\"color:#ddd; font-size:12px\">1841<\/span><\/li><li>Wade RC (2024). <a href=\"https:\/\/doi.org\/10.1002\/jmr.3081\"><span class=\"publication-title\">Editorial: The Journal of Molecular Recognition: Changing of the guard<\/span><\/a>, J of Molecular Recognition 37(3):e3081. <span style=\"color:#ddd; font-size:12px\">1840<\/span><\/li><li>Paiardi G, Milanesi M, Ferraz M, Zimmermann L, Urbinati C, Oreste P, Caccuri F, Chlanda P, Rusnati M, Wade RC (2024). <a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2023.11.1067\"><span class=\"publication-title\">The role of heparin in spike SARS-CoV-2 infection: From a model for heparan sulfates to a starting structure for antivirals<\/span><\/a>, Biophysical Journal 123(3):157a-158a. <span style=\"color:#ddd; font-size:12px\">1842<\/span><\/li><\/ul><h2 id=\"publication-year-2023\">2023<\/h2><ul class=\"publications-list\"><li>Mukesh S, Mukherjee G, Singh R, Steenbuck N, Demidova C, Joshi P, Sangamwar AT, Wade RC (2023). <a href=\"https:\/\/doi.org\/10.1038\/s42004-023-01006-0\"><span class=\"publication-title\">Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance<\/span><\/a>, Commun Chem 6(1),201 <span style=\"color:#ddd; font-size:12px\">1719<\/span><\/li><li>Glaser M, Ritterhof J, Most P, Wade RC (2023). <a href=\"https:\/\/doi.org\/10.1055\/a-2131-2843\"><span class=\"publication-title\">Wird KI neue Medikamente gegen Herzkrankheiten hervorbringen?<\/span><\/a>, Aktuelle Kardiologie 12(06):450-458 <span style=\"color:#ddd; font-size:12px\">1736<\/span><\/li><li>Schimunek J, Seidl P, Elez K, Hempel T, Le T, No\u00e9 F, Olsson S, Raich L, Winter R, Gokcan H, Gusev F, Gutkin EM, Isayev O, Kurnikova MG, Narangoda CH, Zubatyuk R, Bosko IP, Furs KV, Karpenko AD, Kornoushenko YV, Shuldau M, Yushkevich A, Benabderrahmane M, Bousquet-Melou P, Bureau R, Charton B, Cirou B, Gil G, Allen WJ, Sirimulla S, Watowich S, Antonopoulos N, Epitropakis N, Krasoulis A, Pitsikalis V, Theodorakis S, Kozlovskii I, Maliutin A, Medvedev A, Popov P, Zaretckii M, Eghbal-zadeh H, Halmich C, Hochreiter S, Mayr A, Ruch P, Widrich M, Berenger F, Kumar A, Yamanishi Y, Zhang K, Bengio E, Bengio Y, Jain M, Korablyov M, Liu C, Gilles M, Glaab E, Barnsley K, Iyengar SM, Ondrechen MJ, Haupt VJ, Kaiser F, Schroeder M, Pugliese L, Albani S, Athanasiou C, Beccari A, Carloni P, D&#8217;Arrigo G, Gianquinto E, Go\u00dfen J, Hanke A, Joseph BP, Kokh DB, Kovachka S, Manelfi C, Mukherjee G, Mu\u00f1iz-Chicharro A, Musiani F, Nunes-Alves A, Paiardi G, Rossetti G, Sadiq SK, Spyrakis F, Talarico C, Tsengenes A, Wade R, Copeland C, Gaiser J, Olson DR, Roy A, Venkatraman V, Wheeler TJ, Arthanari H, Blaschitz K, Cespugli M, Durmaz V, Fackeldey K, Fischer PD, Gorgulla C, Gruber C, Gruber K, Hetmann M, Kinney JE, Das KMP, Pandita S, Singh A, Steinkellner G, Tesseyre G, Wagner G, Wang Z, Yust RJ, Druzhilovskiy DS, Filimonov D, Pogodin PV, Poroikov V, Rudik AV, Stolbov LA, Veselovsky AV, Rosa MD, Simone GD, Gulotta MR, Lombino J, Mekni N, Perricone U, Casini A, Embree A, Gordon DB, Lei D, Pratt K, Voigt CA, Chen K, Jacob Y, Krischuns T, Lafaye P, Zettor A, Rodr\u00edguez ML, White KM, Fearon D, Delft Fv, Walsh MA, Horvath D, Brooks CL, Falsafi B, Ford B, Garc\u00eda-Sastre A, Lee SY, Naffakh N, Varnek A, Klambauer G, Hermans TM (2023). <a href=\"https:\/\/doi.org\/10.1002\/minf.202300262\"><span class=\"publication-title\">A community effort in SARS\u2010CoV\u20102 drug discovery<\/span><\/a>, Molecular Informatics 43(1):e202300262. <span style=\"color:#ddd; font-size:12px\">1723<\/span><\/li><li>Roussaki M, Magoulas GE, Fotopoulou T, Santarem N, Barrias E, P\u00f6hner I, Luelmo S, Afroudakis P, Georgikopoulou K, Nevado PT, Eick J, Bifeld E, Corral MJ, Jim\u00e9nez-Ant\u00f3n MD, Ellinger B, Kuzikov M, Fragiadaki I, Scoulica E, Gul S, Clos J, Prousis KC, Torrado JJ, Alunda JM, Wade RC, Souza Wd, Silva ACd, Calogeropoulou T (2023). <a href=\"https:\/\/doi.org\/10.1016\/j.bioorg.2023.106615\"><span class=\"publication-title\">Design, synthesis and biological evaluation of antiparasitic dinitroaniline-ether phospholipid hybrids<\/span><\/a>, Bioorganic Chemistry 138:106615 <span style=\"color:#ddd; font-size:12px\">1677<\/span><\/li><li>Viviani LG, Kokh DB, Wade RC, Amaral AT (2023). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.3c01068\"><span class=\"publication-title\">Molecular Dynamics Simulations of the Human Ecto-5\u2032-Nucleotidase (h-ecto-5\u2032-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics<\/span><\/a>, J. Chem. Inf. Model. 63(15):4691-4707 <span style=\"color:#ddd; font-size:12px\">1690<\/span><\/li><li>Gomez GM, D\u2019Arrigo G, Sanchez CP, Berger F, Wade RC, Lanzer M (2023). <a href=\"https:\/\/doi.org\/10.1371\/journal.ppat.1011436\"><span class=\"publication-title\">PfCRT mutations conferring piperaquine resistance in falciparum malaria shape the kinetics of quinoline drug binding and transport<\/span><\/a>, PLoS Pathog 19(6):e1011436 <span style=\"color:#ddd; font-size:12px\">1683<\/span><\/li><li>Mu\u00f1iz\u2010Chicharro A, Votapka LW, Amaro RE, Wade RC (2023). <a href=\"https:\/\/doi.org\/10.1002\/wcms.1649\"><span class=\"publication-title\">Brownian dynamics simulations of biomolecular diffusional association processes<\/span><\/a>, WIREs Comput Mol Sci 13(3),e1649 <span style=\"color:#ddd; font-size:12px\">1555<\/span><\/li><li>Cabezudo AC, Athanasiou C, Tsengenes A, Wade RC (2023). <a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.2c00950\"><span class=\"publication-title\">Scaling Protein\u2013Water Interactions in the Martini 3 Coarse-Grained Force Field to Simulate Transmembrane Helix Dimers in Different Lipid Environments<\/span><\/a>, J. Chem. Theory Comput. 19(7):2109-2119 <span style=\"color:#ddd; font-size:12px\">1635<\/span><\/li><li>Perez S, Makshakova O, Angulo J, Bedini E, Bisio A, Paz JLd, Fadda E, Guerrini M, Hricovini M, Hricovini M, Lisacek F, Nieto PM, Pagel K, Pairardi G, Richter R, Samsonov SA, Viv\u00e8s RA, Nikitovic D, Blum SR (2023). <a href=\"https:\/\/doi.org\/10.1021\/jacsau.2c00569\"><span class=\"publication-title\">Glycosaminoglycans: What Remains To Be Deciphered?<\/span><\/a>, JACS Au 3(3):628-656 <span style=\"color:#ddd; font-size:12px\">1636<\/span><\/li><li>Ferraz MVF, Neto JCS, Lins RD, Teixeira ES (2023). <a href=\"https:\/\/doi.org\/10.1039\/D2CP05644E\"><span class=\"publication-title\">An artificial neural network model to predict structure-based protein\u2013protein free energy of binding from Rosetta-calculated properties<\/span><\/a>, Phys. Chem. Chem. Phys. 25(10):7257-7267 <span style=\"color:#ddd; font-size:12px\">1784<\/span><\/li><li>Rahman MT, Koski MK, Panecka-Hofman J, Schmitz W, Kastaniotis AJ, Wade RC, Wierenga RK, Hiltunen JK, Autio KJ (2023). <a href=\"https:\/\/doi.org\/10.1038\/s41467-023-36358-7\"><span class=\"publication-title\">An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration<\/span><\/a>, Nat Commun 14(1):619. <span style=\"color:#ddd; font-size:12px\">1583<\/span><\/li><li>Keulen SCv, Martin J, Colizzi F, Frezza E, Trpevski D, Diaz NC, Vidossich P, Rothlisberger U, Kotaleski JH, Wade RC, Carloni P (2023). <a href=\"https:\/\/doi.org\/10.1002\/wcms.1623\"><span class=\"publication-title\">Multiscale molecular simulations to investigate adenylyl cyclase\u2010based signaling in the brain<\/span><\/a>, WIREs Comput Mol Sci 13(1),e1623 <span style=\"color:#ddd; font-size:12px\">1493<\/span><\/li><\/ul><h2 id=\"publication-year-2022\">2022<\/h2><ul class=\"publications-list\"><li>Costantino L, Ferrari S, Santucci M, Salo-Ahen OMH, Carosati E, Franchini S, Lauriola A, Pozzi C, Trande M, Gozzi G, Saxena P, Cannazza G, Losi L, Cardinale D, Venturelli A, Quotadamo A, Linciano P, Tagliazucchi L, Moschella MG, Guerrini R, Pacifico S, Luciani R, Genovese F, Henrich S, Alboni S, Santarem N, Cordeiro AdS, Giovannetti E, Peters GJ, Pinton P, Rimessi A, Cruciani G, Stroud RM, Wade RC, Mangani S, Marverti G, D&#8217;Arca D, Ponterini G, Costi MP (2022). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/36475542\"><span class=\"publication-title\">Destabilizers of the thymidylate synthase homodimer accelerate its proteasomal degradation and inhibit cancer growth.<\/span><\/a>, Elife. 2022 Dec 7;11:e73862. doi: 10.7554\/eLife.73862. <span style=\"color:#ddd; font-size:12px\">1557<\/span><\/li><li>Schmidt H, Mauer K, Glaser M, Dezfuli BS, Hellmann SL, Gomes ALS, Butter F, Wade RC, Hankeln T, Herlyn H (2022). <a href=\"https:\/\/doi.org\/10.1186\/s12864-022-08882-1\"><span class=\"publication-title\">Identification of antiparasitic drug targets using a multi-omics workflow in the acanthocephalan model<\/span><\/a>, BMC Genomics 23(1),677 <span style=\"color:#ddd; font-size:12px\">1513<\/span><\/li><li>Mendes MFdA, Bragatte MdS, Vianna P, Freitas MVd, P\u00f6hner I, Richter S, Wade RC, Salzano FM, Vieira GF (2022). <a href=\"https:\/\/doi.org\/10.3389\/fimmu.2022.930590\"><span class=\"publication-title\">MatchTope: A tool to predict the cross reactivity of peptides complexed with Major Histocompatibility Complex I<\/span><\/a>, Front. Immunol. 13,930590 <span style=\"color:#ddd; font-size:12px\">1547<\/span><\/li><li>Dey D, Nunes-Alves A, Wade RC, Schreiber G (2022). <a href=\"https:\/\/doi.org\/10.1016\/j.isci.2022.105088\"><span class=\"publication-title\">Diffusion of small molecule drugs is affected by surface interactions and crowder proteins<\/span><\/a>, iScience 25(10):105088 <span style=\"color:#ddd; font-size:12px\">1599<\/span><\/li><li>Panecka-Hofman J, Poehner I, Wade RC (2022). <a href=\"https:\/\/doi.org\/10.1080\/17460441.2022.2113776\"><span class=\"publication-title\">Anti-trypanosomatid structure-based drug design \u2013 lessons learned from targeting the folate pathway<\/span><\/a>, Expert Opinion on Drug Discovery 17(9):1029-1045 <span style=\"color:#ddd; font-size:12px\">1514<\/span><\/li><li>Toral-Lopez A, Kokh DB, Marin EG, Wade RC, Godoy A (2022). <a href=\"https:\/\/doi.org\/10.1039\/D2NA00357K\"><span class=\"publication-title\">Graphene BioFET sensors for SARS-CoV-2 detection: a multiscale simulation approach<\/span><\/a>, Nanoscale Adv. 4(14):3065-3072 <span style=\"color:#ddd; font-size:12px\">1511<\/span><\/li><li>P\u00f6hner I, Quotadamo A, Panecka-Hofman J, Luciani R, Santucci M, Linciano P, Landi G, Pisa FD, Iacono LD, Pozzi C, Mangani S, Gul S, Witt G, Ellinger B, Kuzikov M, Santarem N, Cordeiro-da-Silva A, Costi MP, Venturelli A, Wade RC (2022). <a href=\"https:\/\/doi.org\/10.1021\/acs.jmedchem.2c00232\"><span class=\"publication-title\">Multitarget, Selective Compound Design Yields Potent Inhibitors of a Kinetoplastid Pteridine Reductase 1<\/span><\/a>, J. Med. Chem. 65(13):9011-9033 <span style=\"color:#ddd; font-size:12px\">1494<\/span><\/li><li>Eriksson O, Bhalla US, Blackwell KT, Crook SM, Keller D, Kramer A, Linne M, Saudargien\u0117 A, Wade RC, Kotaleski JH (2022). <a href=\"https:\/\/doi.org\/10.7554\/eLife.69013\"><span class=\"publication-title\">Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows<\/span><\/a>, eLife 11,e69013 <span style=\"color:#ddd; font-size:12px\">1495<\/span><\/li><li>Rusnati M, Paiardi G, Tobia C, Urbinati C, Lodola A, D\u2019Ursi P, Corrado M, Castelli R, Wade RC, Tognolini M, Chiodelli P (2022). <a href=\"https:\/\/doi.org\/10.1038\/s41417-021-00379-5\"><span class=\"publication-title\">Cholenic acid derivative UniPR1331 impairs tumor angiogenesis via blockade of VEGF\/VEGFR2 in addition to Eph\/ephrin<\/span><\/a>, Cancer Gene Ther 29(7):908-917 <span style=\"color:#ddd; font-size:12px\">1283<\/span><\/li><li>Rogdakis T, Charou D, Latorrata A, Papadimitriou E, Tsengenes A, Athanasiou C, Papadopoulou M, Chalikiopoulou C, Katsila T, Ramos I, Prousis KC, Wade RC, Sidiropoulou K, Calogeropoulou T, Gravanis A, Charalampopoulos I (2022). <a href=\"https:\/\/doi.org\/10.3390\/biomedicines10030614\"><span class=\"publication-title\">Development and Biological Characterization of a Novel Selective TrkA Agonist with Neuroprotective Properties against Amyloid Toxicity<\/span><\/a>, Biomedicines 10(3):614 <span style=\"color:#ddd; font-size:12px\">1470<\/span><\/li><li>Eisenberg P, Albert L, Teuffel J, Zitzow E, Michaelis C, Jarick J, Sehlke C, Gro\u00dfe L, Bader N, Nunes-Alves A, Kreikemeyer B, Schindelin H, Wade RC, Fiedler T (2022). <a href=\"https:\/\/doi.org\/10.3389\/fmicb.2022.802427\"><span class=\"publication-title\">The Non-phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase GapN Is a Potential New Drug Target in Streptococcus pyogenes<\/span><\/a>, Front. Microbiol. 13,802427 <span style=\"color:#ddd; font-size:12px\">1448<\/span><\/li><li>Paiardi G, Richter S, Oreste P, Urbinati C, Rusnati M, Wade RC (2022). <a href=\"https:\/\/doi.org\/10.1016\/j.jbc.2021.101507\"><span class=\"publication-title\">The binding of heparin to spike glycoprotein inhibits SARS-CoV-2 infection by three mechanisms<\/span><\/a>, Journal of Biological Chemistry 298(2):101507 <span style=\"color:#ddd; font-size:12px\">1437<\/span><\/li><\/ul><h2 id=\"publication-year-2021\">2021<\/h2><ul class=\"publications-list\"><li>Sadiq SK, Chicharro AM, Friedrich P, Wade RC (2021). <a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.1c00673\"><span class=\"publication-title\">Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics Simulations<\/span><\/a>, J. Chem. Theory Comput. 17(12):7912-7929 <span style=\"color:#ddd; font-size:12px\">1305<\/span><\/li><li>Mukherjee G, Nandekar PP, Wade RC (2021). <a href=\"https:\/\/doi.org\/10.1038\/s42003-020-01568-y\"><span class=\"publication-title\">An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase<\/span><\/a>, Commun Biol 4(1),55 <span style=\"color:#ddd; font-size:12px\">1165<\/span><\/li><li>Aslam M, Kandasamy N, Ullah A, Paramasivam N, \u00d6zt\u00fcrk MA, Naureen S, Arshad A, Badshah M, Khan K, Wajid M, Abbasi R, Ilyas M, Eils R, Schlesner M, Wade RC, Ahmad N, Engelhardt Jv (2021). <a href=\"https:\/\/doi.org\/10.1038\/s41525-020-00163-8\"><span class=\"publication-title\">Putative second hit rare genetic variants in families with seemingly GBA-associated Parkinson\u2019s disease<\/span><\/a>, npj Genom. Med. 6(1),2 <span style=\"color:#ddd; font-size:12px\">1208<\/span><\/li><li>Bianciotto M, Gkeka P, Kokh DB, Wade RC, Minoux H (2021). <a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.1c00453\"><span class=\"publication-title\">Contact Map Fingerprints of Protein\u2013Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics<\/span><\/a>, J. Chem. Theory Comput. 17(10):6522-6535 <span style=\"color:#ddd; font-size:12px\">1280<\/span><\/li><li>Kokh DB, Wade RC (2021). <a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.1c00641\"><span class=\"publication-title\">G Protein-Coupled Receptor\u2013Ligand Dissociation Rates and Mechanisms from \u03c4RAMD Simulations<\/span><\/a>, J. Chem. Theory Comput. 17(10):6610-6623 <span style=\"color:#ddd; font-size:12px\">1281<\/span><\/li><li>De M, \u00d6zt\u00fcrk MA, Isbaner S, T\u00f3th K, Wade RC (2021). <a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2021.07.012\"><span class=\"publication-title\">DNA sequence-dependent positioning of the linker histone in a nucleosome: A single-pair FRET study<\/span><\/a>, Biophysical Journal 120(17):3747-3763 <span style=\"color:#ddd; font-size:12px\">1276<\/span><\/li><li>Nunes-Alves A, Ormersbach F, Wade RC (2021). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.1c00639\"><span class=\"publication-title\">Prediction of the Drug\u2013Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis<\/span><\/a>, J. Chem. Inf. Model. 61(7):3708-3721 <span style=\"color:#ddd; font-size:12px\">1275<\/span><\/li><li>Gossen J, Albani S, Hanke A, Joseph BP, Bergh C, Kuzikov M, Costanzi E, Manelfi C, Storici P, Gribbon P, Beccari AR, Talarico C, Spyrakis F, Lindahl E, Zaliani A, Carloni P, Wade RC, Musiani F, Kokh DB, Rossetti G (2021). <a href=\"https:\/\/doi.org\/10.1021\/acsptsci.0c00215\"><span class=\"publication-title\">A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics<\/span><\/a>, ACS Pharmacol. Transl. Sci. 4(3):1079-1095 <span style=\"color:#ddd; font-size:12px\">1253<\/span><\/li><li>Reinhardt M, Bruce NJ, Kokh DB, Wade RC (2021). <a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.0c01312\"><span class=\"publication-title\">Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics<\/span><\/a>, J. Chem. Theory Comput. 17(6):3510-3524 <span style=\"color:#ddd; font-size:12px\">1274<\/span><\/li><li>Glaser M, Bruce NJ, Han SB, Wade RC (2021). <a href=\"https:\/\/doi.org\/10.1021\/acs.jpcb.1c00902\"><span class=\"publication-title\">Simulation of the Positive Inotropic Peptide S100A1ct in Aqueous Environment by Gaussian Accelerated Molecular Dynamics<\/span><\/a>, J. Phys. Chem. B 125(18):4654-4666 <span style=\"color:#ddd; font-size:12px\">1267<\/span><\/li><li>Berger B, Amaral M, Kokh DB, Nunes-Alves A, Musil D, Heinrich T, Schr\u00f6der M, Neil R, Wang J, Navratilova I, Bomke J, Elkins JM, M\u00fcller S, Frech M, Wade RC, Knapp S (2021). <a href=\"https:\/\/doi.org\/10.1016\/j.chembiol.2021.01.003\"><span class=\"publication-title\">Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2<\/span><\/a>, Cell Chemical Biology 28(5):686-698.e7 <span style=\"color:#ddd; font-size:12px\">1215<\/span><\/li><li>Paiardi G, Milanesi M, Wade RC, D\u2019Ursi P, Rusnati M (2021). <a href=\"https:\/\/doi.org\/10.3390\/biom11050739\"><span class=\"publication-title\">A Bittersweet Computational Journey among Glycosaminoglycans<\/span><\/a>, Biomolecules 11(5):739 <span style=\"color:#ddd; font-size:12px\">1273<\/span><\/li><li>Dey D, Marciano S, Nunes-Alves A, Kiss V, Wade RC, Schreiber G (2021). <a href=\"https:\/\/doi.org\/10.1016\/j.jmb.2021.166898\"><span class=\"publication-title\">Line-FRAP, A Versatile Method to Measure Diffusion Rates In Vitro and In Vivo<\/span><\/a>, Journal of Molecular Biology 433(9):166898 <span style=\"color:#ddd; font-size:12px\">1224<\/span><\/li><li>Salo-Ahen OMH, Alanko I, Bhadane R, Bonvin AMJJ, Honorato RV, Hossain S, Juffer AH, Kabedev A, Lahtela-Kakkonen M, Larsen AS, Lescrinier E, Marimuthu P, Mirza MU, Mustafa G, Nunes-Alves A, Pantsar T, Saadabadi A, Singaravelu K, Vanmeert M (2021). <a href=\"https:\/\/doi.org\/10.3390\/pr9010071\"><span class=\"publication-title\">Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development<\/span><\/a>, Processes 9(1):71 <span style=\"color:#ddd; font-size:12px\">1162<\/span><\/li><li>Moreau CA, Quadt KA, Piirainen H, Kumar H, Bhargav SP, Strauss L, Tolia NH, Wade RC, Spatz JP, Kursula I, Frischknecht F (2021). <a href=\"https:\/\/doi.org\/10.1242\/jcs.233775\"><span class=\"publication-title\">A function of profilin in force generation during malaria parasite motility that is independent of actin binding<\/span><\/a>, J Cell Sci 134(5):jcs233775 <span style=\"color:#ddd; font-size:12px\">1214<\/span><\/li><li>Ganotra GK, Nunes-Alves A, Wade RC (2021). <a href=\"https:\/\/doi.org\/10.1007\/978-1-0716-1209-5_10\"><span class=\"publication-title\">A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time<\/span><\/a>, In &#8222;Protein-Ligand Interactions and Drug Design&#8220;,  Methods in Molecular Biology (MIMB), 2266:171-186 <span style=\"color:#ddd; font-size:12px\">1252<\/span><\/li><li>Nunes-Alves A, Kokh DB, Wade RC (2021). <a href=\"https:\/\/doi.org\/10.1016\/j.crstbi.2021.04.001\"><span class=\"publication-title\">Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from \u03c4RAMD simulations<\/span><\/a>, Current Research in Structural Biology 3:106-111 <span style=\"color:#ddd; font-size:12px\">1268<\/span><\/li><\/ul><h2 id=\"publication-year-2020\">2020<\/h2><ul class=\"publications-list\"><li>Nunes-Alves A, Mazzolari A, Merz KM (2020). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.0c01248\"><span class=\"publication-title\">What Makes a Paper Be Highly Cited? 60 Years of the\n              Journal of Chemical Information and Modeling<\/span><\/a>, J. Chem. Inf. Model. 60(12):5866-5867 <span style=\"color:#ddd; font-size:12px\">1161<\/span><\/li><li>Mustafa G, Nandekar PP, Mukherjee G, Bruce NJ, Wade RC (2020). <a href=\"https:\/\/doi.org\/10.1038\/s41598-020-64129-7\"><span class=\"publication-title\">The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics<\/span><\/a>, Sci Rep 10(1),7284 <span style=\"color:#ddd; font-size:12px\">1132<\/span><\/li><li>\u00d6zt\u00fcrk MA, Wade RC (2020). <a href=\"https:\/\/doi.org\/10.1016\/j.bbagen.2020.129653\"><span class=\"publication-title\">Computation of FRAP recovery times for linker histone \u2013 chromatin binding on the basis of Brownian dynamics simulations<\/span><\/a>, Biochimica et Biophysica Acta (BBA) &#8211; General Subjects 1864(10):129653 <span style=\"color:#ddd; font-size:12px\">1135<\/span><\/li><li>Nunes-Alves A, Kokh DB, Wade RC (2020). <a href=\"https:\/\/doi.org\/10.1016\/j.sbi.2020.06.022\"><span class=\"publication-title\">Recent progress in molecular simulation methods for drug binding kinetics<\/span><\/a>, Current Opinion in Structural Biology 64:126-133 <span style=\"color:#ddd; font-size:12px\">1138<\/span><\/li><li>Kokh DB, Doser B, Richter S, Ormersbach F, Cheng X, Wade RC (2020). <a href=\"https:\/\/doi.org\/10.1063\/5.0019088\"><span class=\"publication-title\">A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories<\/span><\/a>, J. Chem. Phys. 153(12):125102 <span style=\"color:#ddd; font-size:12px\">1142<\/span><\/li><li>Mazzolari A, Nunes-Alves A, Wahab HA, Amaro RE, Cournia Z, Merz KM (2020). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.0c00636\"><span class=\"publication-title\">Impact of the\r\n              Journal of Chemical Information and Modeling\r\n              Special Issue on Women in Computational Chemistry<\/span><\/a>, J. Chem. Inf. Model. 60(7):3328-3330 <span style=\"color:#ddd; font-size:12px\">1137<\/span><\/li><li>Weidner P, S\u00f6hn M, Schroeder T, Helm L, Hauber V, Gutting T, Betge J, R\u00f6cken C, Rohrbacher FN, Pattabiraman VR, Bode JW, Seger R, Saar D, Nunes-Alves A, Wade RC, Ebert MPA, Burgermeister E (2020). <a href=\"https:\/\/doi.org\/10.1038\/s41389-020-0238-8\"><span class=\"publication-title\">Myotubularin-related protein 7 activates peroxisome proliferator-activated receptor-gamma<\/span><\/a>, Oncogenesis 9(6),59 <span style=\"color:#ddd; font-size:12px\">1143<\/span><\/li><li>Sadiq SK (2020). <a href=\"https:\/\/doi.org\/10.3390\/catal10060684\"><span class=\"publication-title\">Fine-Tuning of Sequence Specificity by Near Attack Conformations in Enzyme-Catalyzed Peptide Hydrolysis<\/span><\/a>, Catalysts 10(6):684 <span style=\"color:#ddd; font-size:12px\">1209<\/span><\/li><li>Diestelkoetter\u2010Bachert P, Beck R, Reckmann I, Hellwig A, Garcia\u2010Saez A, Zelman\u2010Hopf M, Hanke A, Alves AN, Wade RC, Mayer MP, Wieland F (2020). <a href=\"https:\/\/doi.org\/10.1002\/1873-3468.13808\"><span class=\"publication-title\">Structural characterization of an Arf dimer interface: molecular mechanism of Arf\u2010dependent membrane scission<\/span><\/a>, FEBS Lett,1873-3468.13808 <span style=\"color:#ddd; font-size:12px\">1134<\/span><\/li><li>\u00d6zt\u00fcrk MA, De M, Cojocaru V, Wade RC (2020). <a href=\"https:\/\/doi.org\/10.1146\/annurev-physchem-071119-040043\"><span class=\"publication-title\">Chromatosome Structure and Dynamics from Molecular Simulations<\/span><\/a>, Annu. Rev. Phys. Chem. 71(1):101-119 <span style=\"color:#ddd; font-size:12px\">1007<\/span><\/li><li>Yuan J, Han SB, Richter S, Wade RC, Kokh DB (2020). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.9b01185\"><span class=\"publication-title\">Druggability Assessment in TRAPP Using Machine Learning Approaches<\/span><\/a>, J. Chem. Inf. Model. 60(3):1685-1699 <span style=\"color:#ddd; font-size:12px\">1091<\/span><\/li><li>Holderbach S, Adam L, Jayaram B, Wade RC, Mukherjee G (2020). <a href=\"https:\/\/doi.org\/10.3389\/fmolb.2020.601065\"><span class=\"publication-title\">RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features<\/span><\/a>, Frontiers in Molecular Biosciences 7:393 <span style=\"color:#ddd; font-size:12px\">1159<\/span><\/li><li>Berger B, Amaral M, Kokh DB, Nunes-Alves A, Musil D, Heinrich T, Schr\u00f6der M, Neil R, Wang J, Navratilova I, Bomke J, Elkins JM, M\u00fcller S, Frech M, Wade RC, Knapp S (2020). <a href=\"https:\/\/doi.org\/10.2139\/ssrn.3656604\"><span class=\"publication-title\">Structure-Kinetic-Relationship Reveals the Mechanism of Selectivity of FAK Inhibitors Over PYK2<\/span><\/a>, SSRN Journal <span style=\"color:#ddd; font-size:12px\">1168<\/span><\/li><\/ul><h2 id=\"publication-year-2019\">2019<\/h2><ul class=\"publications-list\"><li>Bruce NJ, Narzi D, Trpevski D, Keulen SCv, Nair AG, R\u00f6thlisberger U, Wade RC, Carloni P, Kotaleski JH (2019). <a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1007382\"><span class=\"publication-title\">Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals<\/span><\/a>, PLoS Comput Biol 15(10):e1007382 <span style=\"color:#ddd; font-size:12px\">544<\/span><\/li><li>Nunes-Alves A (2019). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.9b00764\"><span class=\"publication-title\">From Brazil to Germany: Challenges and Advantages<\/span><\/a>, J. Chem. Inf. Model. 60(2):449-451 <span style=\"color:#ddd; font-size:12px\">742<\/span><\/li><li>Mustafa G, Nandekar PP, Bruce NJ, Wade RC (2019). <a href=\"https:\/\/doi.org\/10.3390\/ijms20184328\"><span class=\"publication-title\">Differing Membrane Interactions of Two Highly Similar Drug-Metabolizing Cytochrome P450 Isoforms: CYP 2C9 and CYP 2C19<\/span><\/a>, IJMS 20(18):4328 <span style=\"color:#ddd; font-size:12px\">935<\/span><\/li><li>Calogeropoulou T, Magoulas GE, P\u00f6hner I, Panecka-Hofman J, Linciano P, Ferrari S, Santarem N, Jim\u00e9nez-Ant\u00f3n MD, Ol\u00edas-Molero AI, Alunda JM, Silva ACd, Wade RC, Costi MP (2019). <a href=\"https:\/\/books.google.de\/books?hl=de&#038;lr=&#038;id=kWytDwAAQBAJ&#038;oi=fnd&#038;pg=PA185&#038;ots=ehRpFv8zRq&#038;sig=TT2vFBq_8HumwBA4pysgq0hzkh0#v=onepage&#038;q&#038;f=false\"><span class=\"publication-title\">Hits and Lead Discovery in the Identification of New Drugs against the Trypanosomatidic Infections<\/span><\/a>, Medicinal Chemistry of Neglected and Tropical Diseases: Advances in the Design and Synthesis of Antimicrobial Agents, Eds Venkatesan Jayaprakash, Daniele Castagnolo, Yusuf \u00d6zkay, Chapter 10, pp 185-231, CRC Press <span style=\"color:#ddd; font-size:12px\">727<\/span><\/li><li>Bruce NJ, Ganotra GK, Richter S, Wade RC (2019). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.9b00485\"><span class=\"publication-title\">KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding<\/span><\/a>, J. Chem. Inf. Model. 59(9):3630-3634 <span style=\"color:#ddd; font-size:12px\">543<\/span><\/li><li>Kokh DB, Kaufmann T, Kister B, Wade RC (2019). <a href=\"https:\/\/doi.org\/10.3389\/fmolb.2019.00036\"><span class=\"publication-title\">Machine Learning Analysis of \u03c4RAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times<\/span><\/a>, Front. Mol. Biosci. 6,36 <span style=\"color:#ddd; font-size:12px\">548<\/span><\/li><li>Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, Cecchini M, Changeux J, Bolhuis PG, Vreede J, Faccioli P, Orioli S, Ravasio R, Yan L, Brito C, Wyart M, Gkeka P, Rivalta I, Palermo G, McCammon JA, Panecka-Hofman J, Wade RC, Pizio AD, Niv MY, Nussinov R, Tsai C, Jang H, Padhorny D, Kozakov D, McLeish T (2019). <a href=\"https:\/\/doi.org\/10.1016\/j.str.2019.01.003\"><span class=\"publication-title\">Allostery in Its Many Disguises: From Theory to Applications<\/span><\/a>, Structure 27(4):566-578 <span style=\"color:#ddd; font-size:12px\">549<\/span><\/li><li>Moraes CB, Witt G, Kuzikov M, Ellinger B, Calogeropoulou T, Prousis KC, Mangani S, Pisa FD, Landi G, Iacono LD, Pozzi C, Freitas-Junior LH, Pascoalino BdS, Bertolacini CP, Behrens B, Keminer O, Leu J, Wolf M, Reinshagen J, Cordeiro-da-Silva A, Santarem N, Venturelli A, Wrigley S, Karunakaran D, Kebede B, P\u00f6hner I, M\u00fcller W, Panecka-Hofman J, Wade RC, Fenske M, Clos J, Alunda JM, Corral MJ, Uliassi E, Bolognesi ML, Linciano P, Quotadamo A, Ferrari S, Santucci M, Borsari C, Costi MP, Gul S (2019). <a href=\"https:\/\/doi.org\/10.1177\/2472555218823171\"><span class=\"publication-title\">Accelerating Drug Discovery Efforts for Trypanosomatidic Infections Using an Integrated Transnational Academic Drug Discovery Platform<\/span><\/a>, SLAS DISCOVERY: Advancing the Science of Drug Discovery 24(3):346-361 <span style=\"color:#ddd; font-size:12px\">1075<\/span><\/li><li>Mustafa G, Nandekar PP, Camp TJ, Bruce NJ, Gregory MC, Sligar SG, Wade RC (2019). <a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2018.12.014\"><span class=\"publication-title\">Influence of Transmembrane Helix Mutations on Cytochrome P450-Membrane Interactions and Function<\/span><\/a>, Biophysical Journal 116(3):419-432 <span style=\"color:#ddd; font-size:12px\">551<\/span><\/li><li>Lyonnais S, Sadiq SK, Lorca-Or\u00f3 C, Dufau L, Nieto-Marquez S, Escriba T, Gabrielli N, Tan X, Ouizougun-Oubari M, Okoronkwo J, Reboud-Ravaux M, Gatell JM, Marquet R, Paillart J, Meyerhans A, Tisn\u00e9 C, Gorelick RJ, Mirambeau G (2019). <a href=\"https:\/\/doi.org\/10.1101\/528638\"><span class=\"publication-title\">The HIV-1 ribonucleoprotein dynamically regulates its condensate behavior and drives acceleration of protease activity through membrane-less granular phase-separation<\/span><\/a>, biorxiv;528638v2,[Preprint] <span style=\"color:#ddd; font-size:12px\">1009<\/span><\/li><li>Schmidt TT, Sharma S, Reyes GX, Gries K, Gross M, Zhao B, Yuan J, Wade R, Chabes A, Hombauer H (2019). <a href=\"https:\/\/doi.org\/10.1093\/nar\/gky1154\"><span class=\"publication-title\">A genetic screen pinpoints ribonucleotide reductase residues that sustain dNTP homeostasis and specifies a highly mutagenic type of dNTP imbalance<\/span><\/a>, Nucleic Acids Research 47(1):237-252 <span style=\"color:#ddd; font-size:12px\">728<\/span><\/li><li>Wade RC, Salo-Ahen O (2019). <a href=\"https:\/\/doi.org\/10.3390\/molecules24020321\"><span class=\"publication-title\">Molecular Modeling in Drug Design<\/span><\/a>, Molecules 24(2):321 <span style=\"color:#ddd; font-size:12px\">552<\/span><\/li><li>Mukherjee G, Nandekar P, Mustafa G, Richter S, Wade RC (2019). <a href=\"https:\/\/doi.org\/10.1007\/978-3-030-13325-2_32\"><span class=\"publication-title\">A Multi-resolution Approach to the Simulation of Protein Complexes in a Membrane Bilayer<\/span><\/a>, High Performance Computing in Science and Engineering &#8218; 18,pp.505-514,Springer International Publishing <span style=\"color:#ddd; font-size:12px\">934<\/span><\/li><\/ul><h2 id=\"publication-year-2018\">2018<\/h2><ul class=\"publications-list\"><li>Ganotra GK, Wade RC (2018). <a href=\"https:\/\/doi.org\/10.1021\/acsmedchemlett.8b00397\"><span class=\"publication-title\">Prediction of Drug\u2013Target Binding Kinetics by Comparative Binding Energy Analysis<\/span><\/a>, ACS Med. Chem. Lett. 9(11):1134-1139 <span style=\"color:#ddd; font-size:12px\">385<\/span><\/li><li>Linciano P, Pozzi C, Iacono Ld, Pisa Fd, Landi G, Bonucci A, Gul S, Kuzikov M, Ellinger B, Witt G, Santarem N, Baptista C, Franco C, Moraes CB, M\u00fcller W, Wittig U, Luciani R, Sesenna A, Quotadamo A, Ferrari S, P\u00f6hner I, Cordeiro-da-Silva A, Mangani S, Costantino L, Costi MP (2018). <a href=\"https:\/\/doi.org\/10.1021\/acs.jmedchem.8b02021\"><span class=\"publication-title\">Enhancement of Benzothiazoles as Pteridine Reductase-1 Inhibitors for the Treatment of Trypanosomatidic Infections<\/span><\/a>, J. Med. Chem. 62(8):3989-4012 <span style=\"color:#ddd; font-size:12px\">1008<\/span><\/li><li>Begolo D, Vincent IM, Giordani F, P\u00f6hner I, Witty MJ, Rowan TG, Bengaly Z, Gillingwater K, Freund Y, Wade RC, Barrett MP, Clayton C (2018). <a href=\"https:\/\/doi.org\/10.1371\/journal.ppat.1007315\"><span class=\"publication-title\">The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing<\/span><\/a>, PLoS Pathog 14(9):e1007315 <span style=\"color:#ddd; font-size:12px\">380<\/span><\/li><li>Sadiq SK, Mirambeau G, Meyerhans A (2018). <a href=\"https:\/\/doi.org\/10.1089\/aid.2018.0111\"><span class=\"publication-title\">Equilibrium model of drug-modulated GagPol-embedded HIV-1 reverse transcriptase dimerization to enhance premature protease activation<\/span><\/a>, AIDS Research and Human Retroviruses 34(9):804-807 <span style=\"color:#ddd; font-size:12px\">389<\/span><\/li><li>\u00d6zt\u00fcrk MA, Cojocaru V, Wade RC (2018). <a href=\"https:\/\/doi.org\/10.1016\/j.str.2018.05.009\"><span class=\"publication-title\">Toward an Ensemble View of Chromatosome Structure: A Paradigm Shift from One to Many<\/span><\/a>, Structure 26(8):1050-1057 <span style=\"color:#ddd; font-size:12px\">384<\/span><\/li><li>Douglas RG, Nandekar P, Aktories J, Kumar H, Weber R, Sattler JM, Singer M, Lepper S, Sadiq SK, Wade RC, Frischknecht F (2018). <a href=\"https:\/\/doi.org\/10.1371\/journal.pbio.2005345\"><span class=\"publication-title\">Inter-subunit interactions drive divergent dynamics in mammalian and textitPlasmodium actin filaments<\/span><\/a>, PLoS Biol 16(7):e2005345 <span style=\"color:#ddd; font-size:12px\">390<\/span><\/li><li>Foerster JM, Poehner I, Ullmann GM (2018). <a href=\"https:\/\/doi.org\/10.1021\/acsomega.8b00572\"><span class=\"publication-title\">MCMap &#8211; A Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions<\/span><\/a>, ACS Omega 3(6):6465-6475 <span style=\"color:#ddd; font-size:12px\">381<\/span><\/li><li>Heroven C, Georgi V, Ganotra GK, Brennan P, Wolfreys F, Wade RC, Fern\u00e1ndez-Montalv\u00e1n AE, Chaikuad A, Knapp S (2018). <a href=\"https:\/\/doi.org\/10.1002\/anie.201801666\"><span class=\"publication-title\">Halogen\u2013Aromatic pi Interactions Modulate Inhibitor Residence Times<\/span><\/a>, Angew. Chem. Int. Ed. 57(24):7220-7224 <span style=\"color:#ddd; font-size:12px\">387<\/span><\/li><li>Heroven C, Georgi V, Ganotra GK, Brennan P, Wolfreys F, Wade RC, Fern\u00e1ndez-Montalv\u00e1n AE, Chaikuad A, Knapp S (2018). <a href=\"https:\/\/doi.org\/10.1002\/ange.201801666\"><span class=\"publication-title\">Halogenaromatische pi-Wechselwirkungen modulieren die Verweilzeit von Inhibitoren<\/span><\/a>, Angew. Chem. 130(24):7338-7343 <span style=\"color:#ddd; font-size:12px\">388<\/span><\/li><li>Sultan CS, Saackel A, Stank A, Fleming T, Fedorova M, Hoffmann R, Wade RC, Hecker M, Wagner AH (2018). <a href=\"https:\/\/doi.org\/10.1016\/j.redox.2018.02.018\"><span class=\"publication-title\">Impact of carbonylation on glutathione peroxidase-1 activity in human hyperglycemic endothelial cells<\/span><\/a>, Redox Biology 16:113-122 <span style=\"color:#ddd; font-size:12px\">392<\/span><\/li><li>Kokh DB, Amaral M, Bomke J, Gr\u00e4dler U, Musil D, Buchstaller H, Dreyer MK, Frech M, Lowinski M, Vallee F, Bianciotto M, Rak A, Wade RC (2018). <a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.8b00230\"><span class=\"publication-title\">Estimation of Drug-Target Residence Times by \u03c4-Random Acceleration Molecular Dynamics Simulations<\/span><\/a>, J. Chem. Theory Comput. 14(7):3859-3869 <span style=\"color:#ddd; font-size:12px\">382<\/span><\/li><li>\u00d6zt\u00fcrk MA, Cojocaru V, Wade RC (2018). <a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2018.04.034\"><span class=\"publication-title\">Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification<\/span><\/a>, Biophysical Journal 114(10):2363-2375 <span style=\"color:#ddd; font-size:12px\">383<\/span><\/li><li>Bruce NJ, Ganotra GK, Kokh DB, Sadiq SK, Wade RC (2018). <a href=\"https:\/\/doi.org\/10.1016\/j.sbi.2017.10.001\"><span class=\"publication-title\">New approaches for computing ligand\u2013receptor binding kinetics<\/span><\/a>, Current Opinion in Structural Biology 49:1-10 <span style=\"color:#ddd; font-size:12px\">386<\/span><\/li><li>Sadiq SK, Wade RC (2018). <a href=\"https:\/\/www.cell.com\/biophysj\/pdf\/S0006-3495%2817%2931588-6.pdf\"><span class=\"publication-title\">Computing Protein-Ligand Binding Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics Simulations<\/span><\/a>, Biophysical Journal 114 (3), 56a <span style=\"color:#ddd; font-size:12px\">729<\/span><\/li><\/ul><h2 id=\"publication-year-2017\">2017<\/h2><ul class=\"publications-list\"><li>Amaral M, Kokh DB, Bomke J, Wegener A, Buchstaller HP, Eggenweiler HM, Matias P, Sirrenberg C, Wade RC, Frech M (2017). <a href=\"https:\/\/doi.org\/10.1038\/s41467-017-02258-w\"><span class=\"publication-title\">Protein conformational flexibility modulates kinetics and thermodynamics of drug binding<\/span><\/a>, Nat Commun 8(1),2276  <span style=\"color:#ddd; font-size:12px\">266<\/span><\/li><li>Farnham A, Kurz C, \u00d6zt\u00fcrk MA, Solbiati M, Myllyntaus O, Meekes J, Pham TM, Paz C, Langiewicz M, Andrews S, Kanninen L, Agbemabiese C, Guler AT, Durieux J, Jasim S, Viessmann O, Frattini S, Yembergenova D, Benito CM, Porte M, Grangeray-Vilmint A, Curiel RP, Rehncrona C, Malas T, Esposito F, Hettne K (2017). <a href=\"https:\/\/doi.org\/10.1186\/s13059-017-1351-7\"><span class=\"publication-title\">Early career researchers want Open Science<\/span><\/a>, Genome Biol 18(1),221 <span style=\"color:#ddd; font-size:12px\">268<\/span><\/li><li>Panecka-Hofman J, P\u00f6hner I, Spyrakis F, Zeppelin T, Pisa FD, Iacono LD, Bonucci A, Quotadamo A, Venturelli A, Mangani S, Costi M, Wade RC (2017). <a href=\"https:\/\/doi.org\/10.1016\/j.bbagen.2017.09.012\"><span class=\"publication-title\">Comparative mapping of on-targets and off-targets for the discovery of anti-trypanosomatid folate pathway inhibitors<\/span><\/a>, Biochimica et Biophysica Acta (BBA) &#8211; General Subjects 1861(12):3215-3230 <span style=\"color:#ddd; font-size:12px\">274<\/span><\/li><li>Rafiullah R, Long AB, Ivanova AA, Ali H, Berkel S, Mustafa G, Paramasivam N, Schlesner M, Wiemann S, Wade RC, Bolthauser E, Blum M, Kahn RA, Caspary T, Rappold GA (2017). <a href=\"https:\/\/doi.org\/10.1038\/s41431-017-0031-0\"><span class=\"publication-title\">A novel homozygous ARL13B variant in patients with Joubert syndrome impairs its guanine nucleotide-exchange factor activity<\/span><\/a>, Eur J Hum Genet 25(12):1324-1334 <span style=\"color:#ddd; font-size:12px\">275<\/span><\/li><li>Linciano P, Dawson A, P\u00f6hner I, Costa DM, S\u00e1 MS, Cordeiro-da-Silva A, Luciani R, Gul S, Witt G, Ellinger B, Kuzikov M, Gribbon P, Reinshagen J, Wolf M, Behrens B, Hannaert V, Michels PAM, Nerini E, Pozzi C, Pisa Fd, Landi G, Santarem N, Ferrari S, Saxena P, Lazzari S, Cannazza G, Freitas-Junior LH, Moraes CB, Pascoalino BS, Alc\u00e2ntara LM, Bertolacini CP, Fontana V, Wittig U, M\u00fcller W, Wade RC, Hunter WN, Mangani S, Costantino L, Costi MP (2017). <a href=\"https:\/\/doi.org\/10.1021\/acsomega.7b00473\"><span class=\"publication-title\">Exploiting the 2-Amino-1,3,4-thiadiazole Scaffold To Inhibit Trypanosoma brucei Pteridine Reductase in Support of Early-Stage Drug Discovery<\/span><\/a>, ACS Omega 2(9):5666-5683 <span style=\"color:#ddd; font-size:12px\">270<\/span><\/li><li>Jedwabny W, Panecka-Hofman J, Dyguda-Kazimierowicz E, Wade RC, Sokalski WA (2017). <a href=\"https:\/\/doi.org\/10.1007\/s10822-017-0035-4\"><span class=\"publication-title\">Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition<\/span><\/a>, J Comput Aided Mol Des 31(8):715-728 <span style=\"color:#ddd; font-size:12px\">269<\/span><\/li><li>Stank A, Kokh DB, Horn M, Sizikova E, Neil R, Panecka J, Richter S, Wade RC (2017). <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkx277\"><span class=\"publication-title\">TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets.<\/span><\/a>, Nucleic Acids Research 45(W1):W325-W330 <span style=\"color:#ddd; font-size:12px\">277<\/span><\/li><li>Schuetz DA, Witte WEAd, Wong YC, Knasmueller B, Richter L, Kokh DB, Sadiq SK, Bosma R, Nederpelt I, Heitman LH, Segala E, Amaral M, Guo D, Andres D, Georgi V, Stoddart LA, Hill S, Cooke RM, Graaf CD, Leurs R, Frech M, Wade RC, Lange ECMd, IJzerman AP, M\u00fcller-Fahrnow A, Ecker GF (2017). <a href=\"https:\/\/doi.org\/10.1016\/j.drudis.2017.02.002\"><span class=\"publication-title\">Kinetics for Drug Discovery: an industry-driven effort to target drug residence time<\/span><\/a>, Drug Discovery Today 22(6):896-911 <span style=\"color:#ddd; font-size:12px\">276<\/span><\/li><li>Moreau CA, Bhargav SP, Kumar H, Quadt KA, Piirainen H, Strauss L, Kehrer J, Streichfuss M, Spatz JP, Wade RC, Kursula I, Frischknecht F (2017). <a href=\"https:\/\/doi.org\/10.1371\/journal.ppat.1006412\"><span class=\"publication-title\">A unique profilin-actin interface is important for malaria parasite motility<\/span><\/a>, PLoS Pathog 13(5):e1006412 <span style=\"color:#ddd; font-size:12px\">271<\/span><\/li><li>Nillegoda NB, Stank A, Malinverni D, Alberts N, Szlachcic A, Barducci A, Rios PDL, Wade RC, Bukau B (2017). <a href=\"https:\/\/doi.org\/10.7554\/eLife.24560\"><span class=\"publication-title\">Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes.<\/span><\/a>, eLife 6,e24560 <span style=\"color:#ddd; font-size:12px\">272<\/span><\/li><li>Pisa FD, Landi G, Iacono LD, Pozzi C, Borsari C, Ferrari S, Santucci M, Santarem N, Cordeiro-da-Silva A, Moraes C, Alcantara L, Fontana V, Freitas-Junior L, Gul S, Kuzikov M, Behrens B, P\u00f6hner I, Wade R, Costi M, Mangani S (2017). <a href=\"https:\/\/doi.org\/10.3390\/molecules22030426\"><span class=\"publication-title\">Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity<\/span><\/a>, Molecules 22(3):426 <span style=\"color:#ddd; font-size:12px\">267<\/span><\/li><li>\u00d6zt\u00fcrk MA, Cojocaru V, Wade RC (2017). <a href=\"https:\/\/doi.org\/10.11588\/heibooks.308.418\"><span class=\"publication-title\">Drosophila melanogaster linker histone (dH1) binding to the nucleosome.<\/span><\/a>, In Proceedings of the 3rd bwHPC-Symposium: Heidelberg 2016, pp. 100-102, Eds: Richling, S. and Baumann, M. and Heuveline, V., Heidelberg University Library, heiBOOKS <span style=\"color:#ddd; font-size:12px\">273<\/span><\/li><\/ul><h2 id=\"publication-year-2016\">2016<\/h2><ul class=\"publications-list\"><li>Tong R, Wade RC, Bruce NJ (2016). <a href=\"https:\/\/doi.org\/10.1002\/prot.25167\"><span class=\"publication-title\">Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties<\/span><\/a>, Proteins 84(12):1844-1858 <span style=\"color:#ddd; font-size:12px\">171<\/span><\/li><li>Sadiq SK (2016). <a href=\"https:\/\/doi.org\/10.1098\/rsta.2016.0148\"><span class=\"publication-title\">Reaction\u2013diffusion basis of retroviral infectivity<\/span><\/a>, Phil. Trans. R. Soc. A 374:20160148 <span style=\"color:#ddd; font-size:12px\">169<\/span><\/li><li>Lensink MF, Velankar S, Kryshtafovych A, Huang S, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Lee GR, Seok C, Qin S, Zhou H, Ritchie DW, Maigret B, Devignes M, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, Zundert Gv, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim H, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jim\u00e9nez-Garc\u00eda B, Moal IH, F\u00e9rnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Carpio CAD, Ichiishi E, Marze N, Kuroda D, Burman SSR, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ (2016). <a href=\"https:\/\/doi.org\/10.1002\/prot.25007\"><span class=\"publication-title\">Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment<\/span><\/a>, Proteins 84:323-348 <span style=\"color:#ddd; font-size:12px\">180<\/span><\/li><li>Ozboyaci M, Martinez M, Wade RC (2016). <a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.6b00350\"><span class=\"publication-title\">An efficient low storage and memory treatment of gridded interaction fields for simulations of macromolecular association<\/span><\/a>, J. Chem. Theory Comput. 12(9):4563-4577 <span style=\"color:#ddd; font-size:12px\">173<\/span><\/li><li>\u00d6zt\u00fcrk MA, Pachov GV, Wade RC, Cojocaru V (2016). <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkw514\"><span class=\"publication-title\">Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome<\/span><\/a>, Nucleic Acids Res 44(14):6599-6613 <span style=\"color:#ddd; font-size:12px\">176<\/span><\/li><li>Borsari C, Luciani R, Pozzi C, Poehner I, Henrich S, Trande M, Cordeiro-da-Silva A, Santarem N, Baptista C, Tait A, Pisa FD, Iacono LD, Landi G, Gul S, Wolf M, Kuzikov M, Ellinger B, Reinshagen J, Witt G, Gribbon P, Kohler M, Keminer O, Behrens B, Costantino L, Nevado PT, Bifeld E, Eick J, Clos J, Torrado J, Jim\u00e9nez-Ant\u00f3n MD, Corral MJ, Alunda JM, Pellati F, Wade RC, Ferrari S, Mangani S, Costi MP (2016). <a href=\"https:\/\/doi.org\/10.1021\/acs.jmedchem.6b00698\"><span class=\"publication-title\">Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs<\/span><\/a>, J. Med. Chem. 59(16):7598-7616 <span style=\"color:#ddd; font-size:12px\">174<\/span><\/li><li>Schibich D, Gloge F, P\u00f6hner I, Bj\u00f6rkholm P, Wade RC, Heijne Gv, Bukau B, Kramer G (2016). <a href=\"https:\/\/doi.org\/10.1038\/nature19070\"><span class=\"publication-title\">Global profiling of SRP interaction with nascent polypeptides<\/span><\/a>, Nature 536(7615):219-223 <span style=\"color:#ddd; font-size:12px\">172<\/span><\/li><li>Stank A, Richter S, Wade RC (2016). <a href=\"https:\/\/doi.org\/10.1093\/protein\/gzw021\"><span class=\"publication-title\">ProSAT+: visualizing sequence annotations on 3D structure<\/span><\/a>, Protein Engineering, Design and Selection 29(8):281-284 <span style=\"color:#ddd; font-size:12px\">178<\/span><\/li><li>Wild K, Bange G, Motiejunas D, Kribelbauer J, Hendricks A, Segnitz B, Wade RC, Sinning I (2016). <a href=\"https:\/\/doi.org\/10.1016\/j.jmb.2016.05.015\"><span class=\"publication-title\">Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex<\/span><\/a>, Journal of Molecular Biology 428(14):2880-2897 <span style=\"color:#ddd; font-size:12px\">177<\/span><\/li><li>Subramanian SR, Singam ERA, Berinski M, Subramanian V, Wade RC (2016). <a href=\"https:\/\/doi.org\/10.1021\/acs.jpcb.6b02573\"><span class=\"publication-title\">Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen<\/span><\/a>, J. Phys. Chem. B 120(33):8580-8589 <span style=\"color:#ddd; font-size:12px\">179<\/span><\/li><li>P\u00f6hner IA, Panecka J, Wade RC (2016). <a href=\"https:\/\/jcheminf.biomedcentral.com\/articles\/10.1186\/s13321-016-0119-5\"><span class=\"publication-title\">What determines docking performance in drug discovery? A case study of PTR1, an anti-parasitic target<\/span><\/a>, Journal of Cheminformatics 2016, 8(Suppl 1):P46 <span style=\"color:#ddd; font-size:12px\">553<\/span><\/li><li>Stank A, Kokh DB, Fuller JC, Wade RC (2016). <a href=\"https:\/\/doi.org\/10.1021\/acs.accounts.5b00516\"><span class=\"publication-title\">Protein Binding Pocket Dynamics<\/span><\/a>, Acc. Chem. Res. 49(5):809-815 <span style=\"color:#ddd; font-size:12px\">181<\/span><\/li><li>Gdynia G, Sauer SW, Kopitz J, Fuchs D, Duglova K, Ruppert T, Miller M, Pahl J, Cerwenka A, Enders M, Mairb\u00e4url H, Kami\u0144ski MM, Penzel R, Zhang C, Fuller JC, Wade RC, Benner A, Chang-Claude J, Brenner H, Hoffmeister M, Zentgraf H, Schirmacher P, Roth W (2016). <a href=\"https:\/\/doi.org\/10.1038\/ncomms10764\"><span class=\"publication-title\">The HMGB1 protein induces a metabolic type of tumour cell death by blocking aerobic respiration<\/span><\/a>, Nat Commun 7(1),10764 <span style=\"color:#ddd; font-size:12px\">735<\/span><\/li><li>Khan KM, Mesaik MA, Abdalla OM, Rahim F, Soomro S, Halim SA, Mustafa G, Ambreen N, Khalid AS, Taha M, Perveen S, Alam MT, Hameed A, Ul-Haq Z, Ullah H, Rehman ZU, Siddiqui RA, Voelter W (2016). <a href=\"https:\/\/doi.org\/10.1016\/j.bioorg.2015.11.004\"><span class=\"publication-title\">The immunomodulation potential of the synthetic derivatives of benzothiazoles: Implications in immune system disorders through in vitro and in silico studies<\/span><\/a>, Bioorganic Chemistry 64:21-28 <span style=\"color:#ddd; font-size:12px\">187<\/span><\/li><li>Rafiullah R, Aslamkhan M, Paramasivam N, Thiel C, Mustafa G, Wiemann S, Schlesner M, Wade RC, Rappold GA, Berkel S (2016). <a href=\"https:\/\/doi.org\/10.1136\/jmedgenet-2015-103179\"><span class=\"publication-title\">Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family<\/span><\/a>, J Med Genet 53(2):138-144 <span style=\"color:#ddd; font-size:12px\">185<\/span><\/li><li>Gundi\u0107 M, Tomi\u0107 A, Wade RC, Matovina M, Kara\u010di\u0107 Z, Kazazi\u0107 S, Tomi\u0107 S (2016). <a href=\"https:\/\/doi.org\/10.5562\/cca2916\"><span class=\"publication-title\">Human DPP III \u2013 Keap1 Interactions: A Combined Experimental And Computational study<\/span><\/a>, Croat. Chem. Acta 2016, 89(2), 217\u2013228 <span style=\"color:#ddd; font-size:12px\">170<\/span><\/li><li>Kokh DB, Czodrowski P, Rippmann F, Wade RC (2016). <a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.6b00101\"><span class=\"publication-title\">Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets<\/span><\/a>, J. Chem. Theory Comput. 12(8):4100-4113 <span style=\"color:#ddd; font-size:12px\">175<\/span><\/li><li>Ozboyaci M, Kokh DB, Wade RC (2016). <a href=\"https:\/\/doi.org\/10.1039\/c6cp00201c\"><span class=\"publication-title\">Three steps to Gold: Mechanism of protein adsorption to a gold surface revealed by Brownian and molecular dynamics simulations<\/span><\/a>, Phys. Chem. Chem. Phys. 18(15):10191-10200 <span style=\"color:#ddd; font-size:12px\">182<\/span><\/li><li>Yu X, Kokh DB, Nandekar P, Mustafa G, Richter S, Wade RC (2016). <a href=\"https:\/\/doi.org\/10.1007\/978-3-319-24633-8_17\"><span class=\"publication-title\">Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer<\/span><\/a>, High Performance Computing in Science and Engineering \u00b415,pp.255-264,Springer International Publishing <span style=\"color:#ddd; font-size:12px\">184<\/span><\/li><li>Ozboyaci M, Kokh DB, Corni S, Wade RC (2016). <a href=\"https:\/\/doi.org\/10.1017\/S0033583515000256\"><span class=\"publication-title\">Modeling and simulation of protein\u2013surface interactions: achievements and challenges<\/span><\/a>, Quart. Rev. Biophys. 49,e4 <span style=\"color:#ddd; font-size:12px\">186<\/span><\/li><li>Yu X, Nandekar P, Mustafa G, Cojocaru V, Lepesheva GI, Wade RC (2016). <a href=\"https:\/\/doi.org\/10.1016\/j.bbagen.2015.10.015\"><span class=\"publication-title\">Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design<\/span><\/a>, Biochimica et Biophysica Acta (BBA) &#8211; General Subjects 1860(1):67-78 <span style=\"color:#ddd; font-size:12px\">188<\/span><\/li><\/ul><h2 id=\"publication-year-2015\">2015<\/h2><ul class=\"publications-list\"><li>Mustafa G, Nandekar PP, Yu X, Wade RC (2015). <a href=\"https:\/\/doi.org\/10.1063\/1.4936909\"><span class=\"publication-title\">On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer<\/span><\/a>, The Journal of Chemical Physics 143(24):243139 <span style=\"color:#ddd; font-size:12px\">555<\/span><\/li><li>Garg D, Skouloubris S, Briffotaux J, Myllykallio H, Wade RC (2015). <a href=\"https:\/\/doi.org\/10.1038\/srep17356\"><span class=\"publication-title\">Conservation and Role of Electrostatics in Thymidylate Synthase<\/span><\/a>, Sci Rep 5(1),17356 <span style=\"color:#ddd; font-size:12px\">556<\/span><\/li><li>Romanowska J, Kokh DB, Wade RC (2015). <a href=\"https:\/\/doi.org\/10.1021\/acs.nanolett.5b03168\"><span class=\"publication-title\">When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces<\/span><\/a>, Nano Lett. 15(11):7508-7513 <span style=\"color:#ddd; font-size:12px\">557<\/span><\/li><li>Liu L, Wade RC, Heermann DW (2015). <a href=\"https:\/\/doi.org\/10.1002\/prot.24845\"><span class=\"publication-title\">A multiscale approach to simulating the conformational properties of unbound multi-C2H2 zinc finger proteins<\/span><\/a>, Proteins 83(9):1604-1615 <span style=\"color:#ddd; font-size:12px\">560<\/span><\/li><li>Martinez M, Bruce NJ, Romanowska J, Kokh DB, Ozboyaci M, Yu X, \u00d6zt\u00fcrk MA, Richter S, Wade RC (2015). <a href=\"https:\/\/doi.org\/10.1002\/jcc.23971\"><span class=\"publication-title\">SDA 7: A modular and parallel implementation of the simulation of diffusional association software<\/span><\/a>, J. Comput. Chem. 36(21):1631-1645 <span style=\"color:#ddd; font-size:12px\">561<\/span><\/li><li>Nillegoda NB, Kirstein J, Szlachcic A, Berynskyy M, Stank A, Stengel F, Arnsburg K, Gao X, Scior A, Aebersold R, Guilbride DL, Wade RC, Morimoto RI, Mayer MP, Bukau B (2015). <a href=\"https:\/\/doi.org\/10.1038\/nature14884\"><span class=\"publication-title\">Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation<\/span><\/a>, Nature 524(7564):247-251 <span style=\"color:#ddd; font-size:12px\">559<\/span><\/li><li>Dinh TV, Bienvenut WV, Linster E, Feldman-Salit A, Jung VA, Meinnel T, Hell R, Giglione C, Wirtz M (2015). <a href=\"https:\/\/doi.org\/10.1002\/pmic.201500025\"><span class=\"publication-title\">Molecular identification and functional characterization of the first N\u03b1-acetyltransferase in plastids by global acetylome profiling<\/span><\/a>, Proteomics 15(14):2426-2435 <span style=\"color:#ddd; font-size:12px\">562<\/span><\/li><li>Yu X, Martinez M, Gable AL, Fuller JC, Bruce NJ, Richter S, Wade RC (2015). <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkv335\"><span class=\"publication-title\">webSDA: a web server to simulate macromolecular diffusional association<\/span><\/a>, Nucleic Acids Res 43(W1):W220-W224 <span style=\"color:#ddd; font-size:12px\">564<\/span><\/li><li>Seybold C, Elserafy M, R\u00fcthnick D, Ozboyaci M, Neuner A, Flottmann B, Heilemann M, Wade RC, Schiebel E (2015). <a href=\"https:\/\/doi.org\/10.1083\/jcb.201412050\"><span class=\"publication-title\">Kar1 binding to Sfi1 C-terminal regions anchors the SPB bridge to the nuclear envelope<\/span><\/a>, The Journal of Cell Biology 209(6):843-861 <span style=\"color:#ddd; font-size:12px\">563<\/span><\/li><li>Romanowska J, Kokh DB, Fuller JC, Wade RC (2015). <a href=\"https:\/\/doi.org\/10.1002\/9783527673025.ch11\"><span class=\"publication-title\">Computational Approaches for Studying Drug Binding Kinetics<\/span><\/a>, Thermodynamics and Kinetics of Drug Binding,pp.211-235,Wiley-VCH Verlag GmbH &#038; Co. KGaA <span style=\"color:#ddd; font-size:12px\">567<\/span><\/li><li>Salo-Ahen OMH, Tochowicz A, Pozzi C, Cardinale D, Ferrari S, Boum Y, Mangani S, Stroud RM, Saxena P, Myllykallio H, Costi MP, Ponterini G, Wade RC (2015). <a href=\"https:\/\/doi.org\/10.1021\/acs.jmedchem.5b00137\"><span class=\"publication-title\">Hotspots in an Obligate Homodimeric Anticancer Target. Structural and Functional Effects of Interfacial Mutations in Human Thymidylate Synthase<\/span><\/a>, J. Med. Chem. 58(8):3572-3581 <span style=\"color:#ddd; font-size:12px\">565<\/span><\/li><li>Fuller JC, Martinez M, Henrich S, Stank A, Richter S, Wade RC (2015). <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btu784\"><span class=\"publication-title\">LigDig: a web server for querying ligand\u2013protein interactions<\/span><\/a>, Bioinformatics 31(7):1147-1149 <span style=\"color:#ddd; font-size:12px\">569<\/span><\/li><li>Bruce NJ, Kokh DB, Ozboyaci M, Wade RC (2015). <a href=\"https:\/\/juser.fz-juelich.de\/record\/188877\/files\/IAS-Band-28-V2.pdf\"><span class=\"publication-title\">Modelling of solvation effects for brownian dynamics simulation of biomolecular recognition.<\/span><\/a>, IAS series 28:259-280 <span style=\"color:#ddd; font-size:12px\">566<\/span><\/li><li>Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BFF, Pawlik A, Blomberg N (2015). <a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1003972\"><span class=\"publication-title\">A Quick Guide for Building a Successful Bioinformatics Community.<\/span><\/a>, PLoS Comput Biol 11(2):e1003972 <span style=\"color:#ddd; font-size:12px\">738<\/span><\/li><li>Yu X, Cojocaru V, Mustafa G, Salo-Ahen OMH, Lepesheva GI, Wade RC (2015). <a href=\"https:\/\/doi.org\/10.1002\/jmr.2412\"><span class=\"publication-title\">Dynamics of CYP51: implications for function and inhibitor design<\/span><\/a>, J. Mol. Recognit. 28(2):59-73 <span style=\"color:#ddd; font-size:12px\">568<\/span><\/li><li>Budd A, Dinkel H, Corpas M, Fuller JC, Rubinat L, Devos DP, Khoueiry PH, F\u00f6rstner KU, Georgatos F, Rowland F, Sharan M, Binder JX, Grace T, Traphagen K, Gristwood A, Wood NT (2015). <a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1003905\"><span class=\"publication-title\">Ten Simple Rules for Organizing an Unconference<\/span><\/a>, PLoS Comput Biol 11(1):e1003905 <span style=\"color:#ddd; font-size:12px\">737<\/span><\/li><li>Rosa M, Kokh DB, Corni S, Wadet R, Felice RD (2015). <a href=\"https:\/\/doi.org\/10.13052\/jsame2245-4551.2015009\"><span class=\"publication-title\">Docking of DNA duplexes on a gold surface<\/span><\/a>, JSAME 2015(1):1-18 <span style=\"color:#ddd; font-size:12px\">554<\/span><\/li><li>Tomi\u0107 A, Berynskyy M, Wade RC, Tomi\u0107 S (2015). <a href=\"https:\/\/doi.org\/10.1039\/C5MB00465A\"><span class=\"publication-title\">Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding<\/span><\/a>, Mol. BioSyst. 11(11):3068-3080 <span style=\"color:#ddd; font-size:12px\">558<\/span><\/li><\/ul><h2 id=\"publication-year-2014\">2014<\/h2><ul class=\"publications-list\"><li>Fuller JC, Martinez M, Wade RC (2014). <a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0104778\"><span class=\"publication-title\">On Calculation of the Electrostatic Potential of a Phosphatidylinositol Phosphate-Containing Phosphatidylcholine Lipid Membrane Accounting for Membrane Dynamics<\/span><\/a>, PLoS ONE 9(8):e104778 <span style=\"color:#ddd; font-size:12px\">571<\/span><\/li><li>Mustafa G, Yu X, Wade RC (2014). <a href=\"https:\/\/doi.org\/10.1002\/9783527673261.ch04\"><span class=\"publication-title\">Drug Metabolism Prediction<\/span><\/a>, Wiley <span style=\"color:#ddd; font-size:12px\">572<\/span><\/li><li>Mereghetti P, Martinez M, Wade RC (2014). <a href=\"https:\/\/doi.org\/10.1186\/2046-1682-7-4\"><span class=\"publication-title\">Long range Debye-H\u00fcckel correction for computation of grid-based electrostatic forces between biomacromolecules<\/span><\/a>, BMC Biophys 7(1):4 <span style=\"color:#ddd; font-size:12px\">570<\/span><\/li><\/ul><h2 id=\"publication-year-2013\">2013<\/h2><ul class=\"publications-list\"><li>Gombos L, Neuner A, Berynskyy M, Fava LL, Wade RC, Sachse C, Schiebel E (2013). <a href=\"https:\/\/doi.org\/10.1038\/ncb2863\"><span class=\"publication-title\">GTP regulates the microtubule nucleation activity of \u03b3-tubulin<\/span><\/a>, Nat Cell Biol 15(11):1317-1327 <span style=\"color:#ddd; font-size:12px\">573<\/span><\/li><li>Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC (2013). <a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1003159\"><span class=\"publication-title\">Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria<\/span><\/a>, PLoS Comput Biol 9(7):e1003159 <span style=\"color:#ddd; font-size:12px\">575<\/span><\/li><li>Feldman-Salit A, Hering S, Messiha HL, Veith N, Cojocaru V, Sieg A, Westerhoff HV, Kreikemeyer B, Wade RC, Fiedler T (2013). <a href=\"https:\/\/doi.org\/10.1074\/jbc.M113.458265\"><span class=\"publication-title\">Regulation of the Activity of Lactate Dehydrogenases from Four Lactic Acid Bacteria<\/span><\/a>, J. Biol. Chem. 288(29):21295-21306 <span style=\"color:#ddd; font-size:12px\">576<\/span><\/li><li>Mereghetti P, Wade RC (2013). <a href=\"https:\/\/doi.org\/10.1063\/1.4794626\"><span class=\"publication-title\">Brownian dynamics simulation of protein diffusion in crowded environments<\/span><\/a>, AIP Conference Proceedings,pp.511-516,American Institute of Physics <span style=\"color:#ddd; font-size:12px\">579<\/span><\/li><li>Sandikci A, Gloge F, Martinez M, Mayer MP, Wade R, Bukau B, Kramer G (2013). <a href=\"https:\/\/doi.org\/10.1038\/nsmb.2615\"><span class=\"publication-title\">Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding<\/span><\/a>, Nat Struct Mol Biol 20(7):843-850 <span style=\"color:#ddd; font-size:12px\">574<\/span><\/li><li>Kokh DB, Richter S, Henrich S, Czodrowski P, Rippmann F, Wade RC (2013). <a href=\"https:\/\/doi.org\/10.1021\/ci4000294\"><span class=\"publication-title\">TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins<\/span><\/a>, J. Chem. Inf. Model. 53(5):1235-1252 <span style=\"color:#ddd; font-size:12px\">577<\/span><\/li><li>Balbo J, Mereghetti P, Herten D, Wade R (2013). <a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2013.02.041\"><span class=\"publication-title\">The Shape of Protein Crowders is a Major Determinant of Protein Diffusion<\/span><\/a>, Biophysical Journal 104(7):1576-1584 <span style=\"color:#ddd; font-size:12px\">578<\/span><\/li><li>Garg D, Beribisky AV, Ponterini G, Ligabue A, Marverti G, Martello A, Costi MP, Sattler M, Wade RC (2013). <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkt098\"><span class=\"publication-title\">Translational repression of thymidylate synthase by targeting its mRNA<\/span><\/a>, Nucleic Acids Research 41(7):4159-4170 <span style=\"color:#ddd; font-size:12px\">581<\/span><\/li><li>Fuller JC, Khoueiry P, Dinkel H, Forslund K, Stamatakis A, Barry J, Budd A, Soldatos TG, Linssen K, Rajput AM (2013). <a href=\"https:\/\/doi.org\/10.1038\/embor.2013.34\"><span class=\"publication-title\">Biggest challenges in bioinformatics<\/span><\/a>, EMBO Rep 14(4):302-304 <span style=\"color:#ddd; font-size:12px\">739<\/span><\/li><li>Ferrari S, Ingrami M, Soragni F, Wade RC, Costi MP (2013). <a href=\"https:\/\/doi.org\/10.1016\/j.bmcl.2012.11.117\"><span class=\"publication-title\">Ligand-based discovery of N-(1,3-dioxo-1H,3H-benzo[de]isochromen-5-yl)-carboxamide and sulfonamide derivatives as thymidylate synthase A inhibitors<\/span><\/a>, Bioorganic &#038; Medicinal Chemistry Letters 23(3):663-668 <span style=\"color:#ddd; font-size:12px\">583<\/span><\/li><li>Yu X, Cojocaru V, Wade RC (2013). <a href=\"https:\/\/doi.org\/10.1002\/bab.1074\"><span class=\"publication-title\">Conformational diversity and ligand tunnels of mammalian cytochrome P450s<\/span><\/a>, Biotechnology and Applied Biochemistry 60(1):134-145 <span style=\"color:#ddd; font-size:12px\">580<\/span><\/li><li>Berynskyy M, Wade RC (2013). <a href=\"https:\/\/doi.org\/10.2174\/1877946811303010006\"><span class=\"publication-title\">Treating Conformational Flexibility in Protein-Protein Docking<\/span><\/a>, CPC 3(1):27-35 <span style=\"color:#ddd; font-size:12px\">582<\/span><\/li><\/ul><h2 id=\"publication-year-2012\">2012<\/h2><ul class=\"publications-list\"><li>Oguchi Y, Kummer E, Seyffer F, Berynskyy M, Anstett B, Zahn R, Wade RC, Mogk A, Bukau B (2012). <a href=\"https:\/\/doi.org\/10.1038\/nsmb.2441\"><span class=\"publication-title\">A tightly regulated molecular toggle controls AAA+ disaggregase<\/span><\/a>, Nat Struct Mol Biol 19(12):1338-1346 <span style=\"color:#ddd; font-size:12px\">584<\/span><\/li><li>Brancolini G, Kokh DB, Calzolai L, Wade RC, Corni S (2012). <a href=\"https:\/\/doi.org\/10.1021\/nn303444b\"><span class=\"publication-title\">Docking of Ubiquitin to Gold Nanoparticles<\/span><\/a>, ACS Nano 6(11):9863-9878 <span style=\"color:#ddd; font-size:12px\">585<\/span><\/li><li>Biedermannov\u00e1 L, Prokop Z, Gora A, Chovancov\u00e1 E, Kov\u00e1cs M, Damborsk\u00fd J, Wade RC (2012). <a href=\"https:\/\/doi.org\/10.1074\/jbc.M112.377853\"><span class=\"publication-title\">A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB<\/span><\/a>, J. Biol. Chem. 287(34):29062-29074 <span style=\"color:#ddd; font-size:12px\">587<\/span><\/li><li>Stein M, Pilli M, Bernauer S, Habermann BH, Zerial M, Wade RC (2012). <a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0034870\"><span class=\"publication-title\">The Interaction Properties of the Human Rab GTPase Family \u2013 A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity<\/span><\/a>, PLoS ONE 7(4):e34870 <span style=\"color:#ddd; font-size:12px\">588<\/span><\/li><li>Mereghetti P, Wade RC (2012). <a href=\"https:\/\/doi.org\/10.1021\/jp212532h\"><span class=\"publication-title\">Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions<\/span><\/a>, J. Phys. Chem. B 116(29):8523-8533 <span style=\"color:#ddd; font-size:12px\">586<\/span><\/li><li>Feldman-Salit A, Wirtz M, Lenherr E, Throm C, Hothorn M, Scheffzek K, Hell R, Wade R (2012). <a href=\"https:\/\/doi.org\/10.1016\/j.str.2011.11.019\"><span class=\"publication-title\">Allosterically Gated Enzyme Dynamics in the Cysteine Synthase Complex Regulate Cysteine Biosynthesis in Arabidopsis thaliana<\/span><\/a>, Structure 20(2):292-302 <span style=\"color:#ddd; font-size:12px\">589<\/span><\/li><li>Cojocaru V, Winn PJ, Wade RC (2012). <a href=\"https:\/\/doi.org\/10.2174\/138920012798918462\"><span class=\"publication-title\">Multiple, Ligand-dependent Routes from the Active Site of Cytochrome P450 2C9<\/span><\/a>, CDM 13(2):143-154 <span style=\"color:#ddd; font-size:12px\">590<\/span><\/li><\/ul><h2 id=\"publication-year-2011\">2011<\/h2><ul class=\"publications-list\"><li>Mereghetti P, Wade RC (2011). <a href=\"https:\/\/doi.org\/10.1186\/2046-1682-4-9\"><span class=\"publication-title\">Diffusion of hydrophobin proteins in solution and interactions with a graphite surface<\/span><\/a>, BMC Biophys 4(1),9 <span style=\"color:#ddd; font-size:12px\">594<\/span><\/li><li>Wade RC (2011). <a href=\"https:\/\/www.spektrum.de\/magazin\/das-biomolekulare-erkennungspuzzle\/1129370\"><span class=\"publication-title\">Das biomolekulare Erkennungspuzzle<\/span><\/a>, Spektrum der Wissenschaft &#8211; Extra, 14 &#8211; 17 <span style=\"color:#ddd; font-size:12px\">740<\/span><\/li><li>Salo-Ahen OMH, Wade RC (2011). <a href=\"https:\/\/doi.org\/10.1002\/prot.23123\"><span class=\"publication-title\">The active-inactive transition of human thymidylate synthase: Targeted molecular dynamics simulations<\/span><\/a>, Proteins 79(10):2886-2899 <span style=\"color:#ddd; font-size:12px\">593<\/span><\/li><li>Cardinale D, Guaitoli G, Tondi D, Luciani R, Henrich S, Salo-Ahen OMH, Ferrari S, Marverti G, Guerrieri D, Ligabue A, Frassineti C, Pozzi C, Mangani S, Fessas D, Guerrini R, Ponterini G, Wade RC, Costi MP (2011). <a href=\"https:\/\/doi.org\/10.1073\/pnas.1104829108\"><span class=\"publication-title\">Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase<\/span><\/a>, Proceedings of the National Academy of Sciences 108(34):E542-E549 <span style=\"color:#ddd; font-size:12px\">591<\/span><\/li><li>Cojocaru V, Balali-Mood K, Sansom MSP, Wade RC (2011). <a href=\"https:\/\/doi.org\/10.1371\/journal.pcbi.1002152\"><span class=\"publication-title\">Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9<\/span><\/a>, PLoS Comput Biol 7(8):e1002152 <span style=\"color:#ddd; font-size:12px\">592<\/span><\/li><li>Pachov GV, Gabdoulline RR, Wade RC (2011). <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkr101\"><span class=\"publication-title\">On the structure and dynamics of the complex of the nucleosome and the linker histone<\/span><\/a>, Nucleic Acids Research 39(12):5255-5263 <span style=\"color:#ddd; font-size:12px\">598<\/span><\/li><li>Sundar RS, Gopalakrishnan R, Wade RC, Subramanian V (2011). <a href=\"https:\/\/doi.org\/10.1021\/jp109133v\"><span class=\"publication-title\">Structural Basis for the Varying Propensities of Different Amino Acids To Adopt the Collagen Conformation<\/span><\/a>, J. Phys. Chem. B 115(11):2593-2607 <span style=\"color:#ddd; font-size:12px\">595<\/span><\/li><li>Kokh DB, Wade RC, Wenzel W (2011). <a href=\"https:\/\/doi.org\/10.1002\/wcms.29\"><span class=\"publication-title\">Receptor flexibility in small-molecule docking calculations<\/span><\/a>, WIREs Comput Mol Sci 1(2):298-314 <span style=\"color:#ddd; font-size:12px\">596<\/span><\/li><li>Cohavi O, Reichmann D, Abramovich R, Tesler AB, Bellapadrona G, Kokh DB, Wade RC, Vaskevich A, Rubinstein I, Schreiber G (2011). <a href=\"https:\/\/doi.org\/10.1002\/chem.201001781\"><span class=\"publication-title\">A Quantitative, Real-Time Assessment of Binding of Peptides and Proteins to Gold Surfaces<\/span><\/a>, Chem. Eur. J. 17(4):1327-1336 <span style=\"color:#ddd; font-size:12px\">600<\/span><\/li><li>Ferrari S, Morandi F, Motiejunas D, Nerini E, Henrich S, Luciani R, Venturelli A, Lazzari S, Calo\u0300 S, Gupta S, Hannaert V, Michels PAM, Wade RC, Costi MP (2011). <a href=\"https:\/\/doi.org\/10.1021\/jm1010572\"><span class=\"publication-title\">Virtual Screening Identification of Nonfolate Compounds, Including a CNS Drug, as Antiparasitic Agents Inhibiting Pteridine Reductase<\/span><\/a>, J. Med. Chem. 54(1):211-221 <span style=\"color:#ddd; font-size:12px\">599<\/span><\/li><li>Mereghetti P, Kokh D, McCammon JA, Wade RC (2011). <a href=\"https:\/\/doi.org\/10.1186\/2046-1682-4-2\"><span class=\"publication-title\">Diffusion and association processes in biological systems: theory, computation and experiment<\/span><\/a>, BMC Biophys 4(1):2 <span style=\"color:#ddd; font-size:12px\">597<\/span><\/li><\/ul><h2 id=\"publication-year-2010\">2010<\/h2><ul class=\"publications-list\"><li>Mereghetti P, Gabdoulline RR, Wade RC (2010). <a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2010.10.035\"><span class=\"publication-title\">Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties<\/span><\/a>, Biophysical Journal 99(11):3782-3791 <span style=\"color:#ddd; font-size:12px\">605<\/span><\/li><li>Kaur-Ghumaan S, Schwartz L, Lomoth R, Stein M, Ott S (2010). <a href=\"https:\/\/doi.org\/10.1002\/anie.201002719\"><span class=\"publication-title\">Catalytic Hydrogen Evolution from Mononuclear Iron(II) Carbonyl Complexes as Minimal Functional Models of the [FeFe] Hydrogenase Active Site<\/span><\/a>, Angewandte Chemie International Edition 49(43):8033-8036 <span style=\"color:#ddd; font-size:12px\">602<\/span><\/li><li>Wirtz M, Birke H, Heeg C, M\u00fcller C, Hosp F, Throm C, K\u00f6nig S, Feldman-Salit A, Rippe K, Petersen G, Wade RC, Rybin V, Scheffzek K, Hell R (2010). <a href=\"https:\/\/doi.org\/10.1074\/jbc.M110.157446\"><span class=\"publication-title\">Structure and Function of the Hetero-oligomeric Cysteine Synthase Complex in Plants<\/span><\/a>, J. Biol. Chem. 285(43):32810-32817 <span style=\"color:#ddd; font-size:12px\">604<\/span><\/li><li>Garg D, Henrich S, Salo-Ahen OMH, Myllykallio H, Costi MP, Wade RC (2010). <a href=\"https:\/\/doi.org\/10.1021\/jm901869w\"><span class=\"publication-title\">Novel Approaches for Targeting Thymidylate Synthase To Overcome the Resistance and Toxicity of Anticancer Drugs<\/span><\/a>, J. Med. Chem. 53(18):6539-6549 <span style=\"color:#ddd; font-size:12px\">606<\/span><\/li><li>Klipp E, Wade RC, Kummer U (2010). <a href=\"https:\/\/doi.org\/10.1016\/j.copbio.2010.05.004\"><span class=\"publication-title\">Biochemical network-based drug-target prediction<\/span><\/a>, Current Opinion in Biotechnology 21(4):511-516 <span style=\"color:#ddd; font-size:12px\">607<\/span><\/li><li>Pachov GV, Gabdoulline RR, Wade RC (2010). <a href=\"https:\/\/doi.org\/10.1142\/9781848163409_0004\"><span class=\"publication-title\">Kinetics of Biomacromolecular Complex Formation: Theory and Experiment<\/span><\/a>, Protein-Protein Complexes,pp.89-118,IMPERIAL COLLEGE PRESS <span style=\"color:#ddd; font-size:12px\">614<\/span><\/li><li>O&#8217;Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ (2010). <a href=\"https:\/\/doi.org\/10.1038\/nmeth.1427\"><span class=\"publication-title\">Visualization of macromolecular structures<\/span><\/a>, Nat Methods 7(S3):S42-S55 <span style=\"color:#ddd; font-size:12px\">609<\/span><\/li><li>Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC (2010). <a href=\"https:\/\/doi.org\/10.1002\/prot.22579\"><span class=\"publication-title\">Comparative binding energy analysis for binding affinity and target selectivity prediction<\/span><\/a>, Proteins 78(1):135-153 <span style=\"color:#ddd; font-size:12px\">615<\/span><\/li><li>Michielin O, Wade RC (2010). <a href=\"https:\/\/doi.org\/10.1002\/jmr.1028\"><span class=\"publication-title\">Foreword Preface to the JMR Special Issue on \u2018Dynamic Aspects of Molecular Recognition\u2019<\/span><\/a>, J. Mol. Recognit., 23: 101-101 <span style=\"color:#ddd; font-size:12px\">670<\/span><\/li><\/ul><h2 id=\"publication-year-2009\">2009<\/h2><ul class=\"publications-list\"><li>Singh PS, Rudbeck HC, Huang P, Ezzaher S, Eriksson L, Stein M, Ott S, Lomoth R (2009). <a href=\"https:\/\/doi.org\/10.1021\/ic9016454\"><span class=\"publication-title\">(I,0) Mixed-Valence State of a Diiron Complex with Pertinence to the [FeFe]-Hydrogenase Active Site: An IR, EPR, and Computational Study<\/span><\/a>, Inorg. Chem. 48(23):10883-10885 <span style=\"color:#ddd; font-size:12px\">618<\/span><\/li><li>Pavlova M, Klvana M, Prokop Z, Chaloupkova R, Banas P, Otyepka M, Wade RC, Tsuda M, Nagata Y, Damborsky J (2009). <a href=\"https:\/\/doi.org\/10.1038\/nchembio.205\"><span class=\"publication-title\">Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate<\/span><\/a>, Nat Chem Biol 5(10):727-733 <span style=\"color:#ddd; font-size:12px\">619<\/span><\/li><li>Klvana M, Pavlova M, Koudelakova T, Chaloupkova R, Dvorak P, Prokop Z, Stsiapanava A, Kuty M, Kuta-Smatanova I, Dohnalek J, Kulhanek P, Wade RC, Damborsky J (2009). <a href=\"https:\/\/doi.org\/10.1016\/j.jmb.2009.06.076\"><span class=\"publication-title\">Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations<\/span><\/a>, Journal of Molecular Biology 392(5):1339-1356 <span style=\"color:#ddd; font-size:12px\">620<\/span><\/li><li>Huang B (2009). <a href=\"https:\/\/doi.org\/10.1089\/omi.2009.0045\"><span class=\"publication-title\">MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction<\/span><\/a>, OMICS: A Journal of Integrative Biology 13(4):325-330 <span style=\"color:#ddd; font-size:12px\">616<\/span><\/li><li>Pachov GV, Gabdoulline RR, Wade RC (2009). <a href=\"https:\/\/doi.org\/10.1201\/9781420070071\"><span class=\"publication-title\">Computational Simulations of Protein\u2013 Protein and Protein\u2013 Nucleic Acid Association<\/span><\/a>, CRC Press <span style=\"color:#ddd; font-size:12px\">622<\/span><\/li><li>M\u00fcller C, Frau MAG, Ballinari D, Colombo S, Bitto A, Martegani E, Airoldi C, van\u2005Neuren AS, Stein M, Weiser J, Battistini C, Peri F (2009). <a href=\"https:\/\/doi.org\/10.1002\/cmdc.200800416\"><span class=\"publication-title\">Design, Synthesis, and Biological Evaluation of Levoglucosenone-Derived Ras Activation Inhibitors<\/span><\/a>, ChemMedChem 4(4):524-528 <span style=\"color:#ddd; font-size:12px\">617<\/span><\/li><li>Pachov GV, Wade RC (2009). <a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2008.12.335\"><span class=\"publication-title\">Docking of a Linker Histone to The Nucleosome With Flexible Linker DNAs<\/span><\/a>, Biophysical Journal 96(3):83a-84a <span style=\"color:#ddd; font-size:12px\">623<\/span><\/li><li>Kokh DB, Huang B, Wade RC, Winn PJ (2009). <a href=\"https:\/\/doi.org\/10.1016\/j.bpj.2008.12.1483\"><span class=\"publication-title\">Modeling of Protein Adsorption on a Metal Surface: Brownian Dynamics Simulations<\/span><\/a>, Biophysical Journal 96(3):298a-299a <span style=\"color:#ddd; font-size:12px\">624<\/span><\/li><li>Feldman-Salit A, Wirtz M, Hell R, Wade RC (2009). <a href=\"https:\/\/doi.org\/10.1016\/j.jmb.2008.08.075\"><span class=\"publication-title\">A Mechanistic Model of the Cysteine Synthase Complex<\/span><\/a>, Journal of Molecular Biology 386(1):37-59 <span style=\"color:#ddd; font-size:12px\">625<\/span><\/li><li>Stein M, Gabdoulline RR, Wade RC (2009). <a href=\"https:\/\/doi.org\/10.1039\/B912398A\"><span class=\"publication-title\">Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields<\/span><\/a>, Mol. BioSyst. 6(1):162-174 <span style=\"color:#ddd; font-size:12px\">612<\/span><\/li><li>Pachov GV, Gabdoulline RR, Wade RC (2009). <span class=\"publication-title\">Computational Simulations of Protein-Protein and Protein-Nucleic Acid Association.<\/span>, In &#8220; Computational Protein-Protein Interactions&#8220;, Eds. R. Nussinov and G. Schreiber, Taylor and Francis Group LLC, Boca Raton:109\u2013128 <span style=\"color:#ddd; font-size:12px\">678<\/span><\/li><li>Cohavi O, Corni S, Rienzo FD, Felice RD, Gottschalk KE, Hoefling M, Kokh D, Molinari E, Schreiber G, Vaskevich A, Wade RC (2009). <a href=\"https:\/\/doi.org\/10.1002\/jmr.993\"><span class=\"publication-title\">Protein\u2013surface interactions: challenging experiments and computations<\/span><\/a>, J. Mol. Recognit.,  23: 259-262 <span style=\"color:#ddd; font-size:12px\">1130<\/span><\/li><li>Henrich S, Salo-Ahen OMH, Huang B, Rippmann FF, Cruciani G, Wade RC (2009). <a href=\"https:\/\/doi.org\/10.1002\/jmr.984\"><span class=\"publication-title\">Computational approaches to identifying and characterizing protein binding sites for ligand design<\/span><\/a>, J. Mol. Recognit., 23: 209-219 <span style=\"color:#ddd; font-size:12px\">1131<\/span><\/li><\/ul><h2 id=\"publication-year-2008\">2008<\/h2><ul class=\"publications-list\"><li>Weidemann A, Richter S, Stein M, Sahle S, Gauges R, Gabdoulline R, Surovtsova I, Semmelrock N, Besson B, Rojas I, Wade R, Kummer U (2008). <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btn207\"><span class=\"publication-title\">SYCAMORE&#8211;a systems biology computational analysis and modeling research environment<\/span><\/a>, Bioinformatics 24(12):1463-1464 <span style=\"color:#ddd; font-size:12px\">630<\/span><\/li><li>Motiejunas D, Gabdoulline R, Wang T, Feldman-Salit A, Johann T, Winn PJ, Wade RC (2008). <a href=\"https:\/\/doi.org\/10.1002\/prot.21867\"><span class=\"publication-title\">Protein-protein docking by simulating the process of association subject to biochemical constraints<\/span><\/a>, Proteins 71(4):1955-1969 <span style=\"color:#ddd; font-size:12px\">632<\/span><\/li><li>Richter S, Wenzel A, Stein M, Gabdoulline RR, Wade RC (2008). <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkn181\"><span class=\"publication-title\">webPIPSA: a web server for the comparison of protein interaction properties<\/span><\/a>, Nucleic Acids Research 36(Web Server):W276-W280 <span style=\"color:#ddd; font-size:12px\">629<\/span><\/li><li>Witan H, Kern A, Koziollek-Drechsler I, Wade R, Behl C, Clement AM (2008). <a href=\"https:\/\/doi.org\/10.1093\/hmg\/ddn025\"><span class=\"publication-title\">Heterodimer formation of wild-type and amyotrophic lateral sclerosis-causing mutant Cu\/Zn-superoxide dismutase induces toxicity independent of protein aggregation<\/span><\/a>, Human Molecular Genetics 17(10):1373-1385 <span style=\"color:#ddd; font-size:12px\">631<\/span><\/li><li>Hegermann J, Halbedel S, Dumke R, Regula J, Gabdoulline RR, Mayer F, St\u00fclke J, Herrmann R (2008). <a href=\"https:\/\/doi.org\/10.1099\/mic.0.2007\/013342-0\"><span class=\"publication-title\">The acidic, glutamine-rich Mpn474 protein of Mycoplasma pneumoniae is surface exposed and covers the complete cell<\/span><\/a>, Microbiology 154(4):1185-1192 <span style=\"color:#ddd; font-size:12px\">628<\/span><\/li><li>Henrich S, Richter S, Wade R (2008). <a href=\"https:\/\/doi.org\/10.1002\/cmdc.200700154\"><span class=\"publication-title\">On the use of PIPSA to Guide Target-Selective Drug Design<\/span><\/a>, ChemMedChem 3(3):413-417 <span style=\"color:#ddd; font-size:12px\">635<\/span><\/li><li>Bauer R, Woelkart K, Salo-Ahen O (2008). <a href=\"https:\/\/doi.org\/10.2174\/156802608783498023\"><span class=\"publication-title\">CB Receptor Ligands from Plants<\/span><\/a>, CTMC 8(3):173-186 <span style=\"color:#ddd; font-size:12px\">626<\/span><\/li><li>Salo-Ahen O (2008). <a href=\"https:\/\/doi.org\/10.2174\/156802608783498069\"><span class=\"publication-title\">Editorial: The Medicinal Chemistry of Agents Targeting the Endogenous Cannabinoid System<\/span><\/a>, CTMC 8(3):172-172 <span style=\"color:#ddd; font-size:12px\">627<\/span><\/li><li>Stein M, Gabdoulline R, Wade R (2008). <a href=\"https:\/\/doi.org\/10.1042\/BST0360051\"><span class=\"publication-title\">Calculating enzyme kinetic parameters from protein structures<\/span><\/a>, Biochemical Society Transactions 36(1):51-54 <span style=\"color:#ddd; font-size:12px\">633<\/span><\/li><\/ul><h2 id=\"publication-year-2007\">2007<\/h2><ul class=\"publications-list\"><li>Feldman-Salit A, Wade RC (2007). <a href=\"https:\/\/doi.org\/10.1002\/9780470048672.wecb354\"><span class=\"publication-title\">Molecular Recognition: Computational Analysis and Modelling<\/span><\/a>,  In Wiley Encyclopedia of Chemical Biology, T.P. Begley (Ed.), 1-10, John Wiley &#038; Sons, Inc. <span style=\"color:#ddd; font-size:12px\">1129<\/span><\/li><li>Wade RC (2007). <a href=\"https:\/\/doi.org\/10.1142\/9789812779458_0018\"><span class=\"publication-title\">Exploring biomolecular recognition by modelling and simulation<\/span><\/a>, Modelling and Simulation in Science,pp.150-153,WORLD SCIENTIFIC <span style=\"color:#ddd; font-size:12px\">640<\/span><\/li><li>L\u00f6scher S, Schwartz L, Stein M, Ott S, Haumann M (2007). <a href=\"https:\/\/doi.org\/10.1021\/ic701255p\"><span class=\"publication-title\">Facilitated Hydride Binding in an Fe\u2212Fe Hydrogenase Active\u2212Site Biomimic Revealed by X-ray Absorption Spectroscopy and DFT Calculations<\/span><\/a>, Inorg. Chem. 46(26):11094-11105 <span style=\"color:#ddd; font-size:12px\">637<\/span><\/li><li>Eilers G, Schwartz L, Stein M, Zampella G, de\u2005Gioia L, Ott S, Lomoth R (2007). <a href=\"https:\/\/doi.org\/10.1002\/chem.200700019\"><span class=\"publication-title\">Ligand versus Metal Protonation of an Iron Hydrogenase Active Site Mimic<\/span><\/a>, Chem. Eur. J. 13(25):7075-7084 <span style=\"color:#ddd; font-size:12px\">636<\/span><\/li><li>Pachov G, Gabdoulline RR, Wade RC (2007). <a href=\"https:\/\/juser.fz-juelich.de\/record\/135931\/files\/NIC222945.pdf\"><span class=\"publication-title\">Simulation of linker histone-chromatin interactions<\/span><\/a>, In From Computational Biophysics to Systems Biology 2007 (CBSB07), Hansmann, Ulrich H.E.; Meinke, Jan; Mohanty, Sandipan; Zimmermann, Olav (Eds.), John von Neumann Institute for Computing, Juelich, NIC Series 36:69-74 <span style=\"color:#ddd; font-size:12px\">641<\/span><\/li><li>.Winn PJ, Zahran M, Wade RC (2007). <a href=\"https:\/\/doi.org\/10.3254\/978-1-58603-792-5-207\"><span class=\"publication-title\">Comparisons of the protein electrostatic potentials as a means to understanding function<\/span><\/a>, Proceedings of the International School of Physics \u201cEnrico Fermi\u201d, (2007) pages 207-219 <span style=\"color:#ddd; font-size:12px\">645<\/span><\/li><li>Stein M, Gabdoulline RR, Besson B, Wade RC (2007). <a href=\"https:\/\/www.beilstein-institut.de\/download\/695\/stein.pdf\"><span class=\"publication-title\">The estimation of kinetic parameters in systems biology by comparing molecular interaction fields of enzymes.<\/span><\/a>, Beilstein Proceedings of the 2nd Conference on Experimental Standard Conditions of Enzyme Characterizations,Ruedesheim, 19-23 March, 2006, (2007) pages 237-253 <span style=\"color:#ddd; font-size:12px\">647<\/span><\/li><li>Cruciani G, Carosati E, Wade RC, Baroni M (2007). <span class=\"publication-title\">Characterization of protein-binding sites and ligands using molecular interaction fields.<\/span>, Comprehensive Medicinal Chemistry II, (2007) volume 4, pages 237-253 <span style=\"color:#ddd; font-size:12px\">650<\/span><\/li><li>Wang T, Wade RC (2007). <a href=\"https:\/\/doi.org\/10.1021\/ct700063c\"><span class=\"publication-title\">On the Use of Elevated Temperature in Simulations To Study Protein Unfolding Mechanisms<\/span><\/a>, J. Chem. Theory Comput. 3(4):1476-1483 <span style=\"color:#ddd; font-size:12px\">642<\/span><\/li><li>Tomi\u0107 S, Berto\u0161a B, Wang T, Wade RC (2007). <a href=\"https:\/\/doi.org\/10.1002\/prot.21321\"><span class=\"publication-title\">COMBINE analysis of the specificity of binding of Ras proteins to their effectors<\/span><\/a>, Proteins 67(2):435-447 <span style=\"color:#ddd; font-size:12px\">644<\/span><\/li><li>Stein M, Gabdoulline RR, Wade RC (2007). <a href=\"https:\/\/doi.org\/10.1016\/j.sbi.2007.03.014\"><span class=\"publication-title\">Bridging from molecular simulation to biochemical networks<\/span><\/a>, Current Opinion in Structural Biology 17(2):166-172 <span style=\"color:#ddd; font-size:12px\">639<\/span><\/li><li>Karyakin A, Motiejunas D, Wade RC, Jung C (2007). <a href=\"https:\/\/doi.org\/10.1016\/j.bbagen.2006.08.020\"><span class=\"publication-title\">FTIR studies of the redox partner interaction in cytochrome P450: The Pdx\u2013P450cam couple<\/span><\/a>, Biochimica et Biophysica Acta (BBA) &#8211; General Subjects 1770(3):420-431 <span style=\"color:#ddd; font-size:12px\">646<\/span><\/li><li>Cojocaru V, Winn PJ, Wade RC (2007). <a href=\"https:\/\/doi.org\/10.1016\/j.bbagen.2006.07.005\"><span class=\"publication-title\">The ins and outs of cytochrome P450s<\/span><\/a>, Biochimica et Biophysica Acta (BBA) &#8211; General Subjects 1770(3):390-401 <span style=\"color:#ddd; font-size:12px\">648<\/span><\/li><li>Gabdoulline RR, Stein M, Wade RC (2007). <a href=\"https:\/\/doi.org\/10.1186\/1471-2105-8-373\"><span class=\"publication-title\">qPIPSA: Relating enzymatic kinetic parameters and interaction fields<\/span><\/a>, BMC Bioinformatics 8(1):373 <span style=\"color:#ddd; font-size:12px\">638<\/span><\/li><li>Winn P, Zahran M, Wade R (2007). <span class=\"publication-title\">Proceedings of the International School of Physics &#8222;Enrico Fermi&#8220; workshop on Protein Folding and Drug Design<\/span>, In Comparisons of Protein Electrostatic Potentials as a Means to Understanding Function <span style=\"color:#ddd; font-size:12px\">733<\/span><\/li><li>Karyakin A, Motiejunas D, Wade R, Jung C (2007). <span class=\"publication-title\">FTIR studies of the redox partner interaction in cytochrome P450:  The Pdx-P450cam couple<\/span>, Biochimica et Biophysica Acta. General Subjects 1770:420\u2013431 <span style=\"color:#ddd; font-size:12px\">745<\/span><\/li><li>Motiejunas D, Wade R (2007). <a href=\"https:\/\/doi.org\/10.1016\/B0-08-045044-X\/00250-9\"><span class=\"publication-title\">Structural, Energetic, and Dynamic Aspects of Ligand\u2013Receptor Interactions<\/span><\/a>, Comprehensive Medicinal Chemistry II,pp.193-213,Elsevier <span style=\"color:#ddd; font-size:12px\">1128<\/span><\/li><\/ul><h2 id=\"publication-year-2006\">2006<\/h2><ul class=\"publications-list\"><li>Stein M, Gabdoulline R, Be\u00dfon B, Wade R (2006). <span class=\"publication-title\">Beilstein Proceedings of the 2nd Conference on \u2019Experimental Standard Conditions of Enzyme Characterizations (ESCEC)\u2019 em Ruedesheim (2007) em<\/span>, In The Estimation of Kinetic Parameters in Systems Biology by Comparing Molecular Interaction Fields of Enzymes, pp. 237\u2013253, 19-23 March <span style=\"color:#ddd; font-size:12px\">746<\/span><\/li><li>Stein M, Gabdoulline RR, Wade RC (2006). <span class=\"publication-title\">Integrating Structural and Kinetic Enzymatic Information in Systems Biology<\/span>, In NIC Workshop 2006  \u2019From Computational Biophysics to Systems Biology\u2019, 6\u20139 June, John von Neumann Institute for Computing, Juelich, vol. 34 of NIC Series, pp. 129\u2013132 <span style=\"color:#ddd; font-size:12px\">689<\/span><\/li><li>K. S, T. W, R.C. W (2006). <span class=\"publication-title\">Molecular Docking<\/span>, In Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, pp. pp1149\u20131153, Ed. Ganten,D. and Ruckpaul, K., Springer <span style=\"color:#ddd; font-size:12px\">690<\/span><\/li><li>Gabdoulline RR, Ulbrich S, Richter S, Wade RC (2006). <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkl216\"><span class=\"publication-title\">ProSAT2-Protein Structure Annotation Server<\/span><\/a>, Nucleic Acids Research 34(Web Server):W79-W83 <span style=\"color:#ddd; font-size:12px\">691<\/span><\/li><li>Hallingb\u00e4ck HR, Gabdoulline RR, Wade RC (2006). <a href=\"https:\/\/doi.org\/10.1021\/bi051510e\"><span class=\"publication-title\">Comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking<\/span><\/a>, Biochemistry 45(9):2940-2950 <span style=\"color:#ddd; font-size:12px\">692<\/span><\/li><li>Spaar A, Dammer C, Gabdoulline RR, Wade RC, Helms V (2006). <a href=\"https:\/\/doi.org\/10.1529\/biophysj.105.075507\"><span class=\"publication-title\">Diffusional encounter of barnase and barstar<\/span><\/a>, Biophysical Journal 90(6):1913-1924 <span style=\"color:#ddd; font-size:12px\">693<\/span><\/li><li>Wang T, Wade RC (2006). <a href=\"https:\/\/doi.org\/10.1021\/ct0501607\"><span class=\"publication-title\">Force Field Effects on a beta-sheet Protein Domain Structure in Thermal Unfolding Simulations<\/span><\/a>, J. Chem. Theory Comput. 2(1):140-148 <span style=\"color:#ddd; font-size:12px\">694<\/span><\/li><li>Jalkanen KJ, J\u00fcrgensen VW, Claussen A, Rahim A, Jensen GM, Wade RC, Nardi F, Jung C, Degtyarenko IM, Nieminen RM, Herrmann F, Knapp-Mohammady M, Niehaus TA, Frimand K, Suhai S (2006). <a href=\"https:\/\/doi.org\/10.1002\/qua.20863\"><span class=\"publication-title\">Use of Vibrational Spectroscopy to Study Protein and DNA Structure, Hydration, and Binding of Biomolecules: A Combined Theoretical and Experimental Approach<\/span><\/a>, Int. J. Quantum Chem. 106(5):1160-1198 <span style=\"color:#ddd; font-size:12px\">695<\/span><\/li><li>Cruciani G, Carosati E, Wade R, Baroni M (2006). <span class=\"publication-title\">Characterization of Protein- Binding Sites and Ligands Using Molecular Interaction Fields<\/span>, In Comprehensive Medicinal Chemistry II, vol. 4, pp. 237\u2013253, Ed. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford <span style=\"color:#ddd; font-size:12px\">747<\/span><\/li><li>Motiejunas D, Wade R (2006). <span class=\"publication-title\">Structural, Energetic and Dynamic Aspects of Ligand-Receptor Interactions<\/span>, In Comprehensive Medicinal Chemistry II, vol. 4, pp. pp.193\u2013213, Ed. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford <span style=\"color:#ddd; font-size:12px\">748<\/span><\/li><li>Stein M, Gabdoulline R, Wade R (2006). <span class=\"publication-title\">From Computational Biophysics to Systems Biology 2006<\/span>, In Integrating Structural and Kinetic Enzymatic Information in Systems Biology, vol. 34 of NIC Series, pp. 129\u2013132, Hansmann, Ulrich H.E.; Meinke, Jan; Mohanty, Sandipan; Zimmermann, Olav (Eds.) <span style=\"color:#ddd; font-size:12px\">749<\/span><\/li><li>Wang T, Wade R (2006). <span class=\"publication-title\">Force Field Effects on a b-sheet Protein Domain Structure in Thermal Unfolding Simulations<\/span>, J Chem Theory and Comput 2:140\u2013148 <span style=\"color:#ddd; font-size:12px\">750<\/span><\/li><\/ul><h2 id=\"publication-year-2005\">2005<\/h2><ul class=\"publications-list\"><li>Wade RC, Motiejunas D, Schleinkofer K, Sudarko PJW, Banerjee A, Kariakin A, Jung C (2005). <a href=\"https:\/\/doi.org\/10.1016\/j.bbapap.2005.07.044\"><span class=\"publication-title\">Multiple molecular recognition mechanisms. Cytochrome P450\u2013A case study<\/span><\/a>, Biochimica et Biophysica Acta (BBA) &#8211; Proteins and Proteomics 1754(1-2):239-244 <span style=\"color:#ddd; font-size:12px\">696<\/span><\/li><li>Wade RC (2005). <span class=\"publication-title\">Calculation and Application of Molecular Interaction Fields<\/span>, In Molecular Interaction Fields. Applications in Drug Discovery and ADME Prediction, pp. Ch. 2, pp27\u201342, Ed. Cruciani, G., Wiley-VCH, Weinheim, ISBN 3-527-31087-8 <span style=\"color:#ddd; font-size:12px\">697<\/span><\/li><li>Schleinkofer K, Sudarko PJW, L\u00fcdemann SK, Wade RC (2005). <a href=\"https:\/\/doi.org\/10.1038\/sj.embor.7400420\"><span class=\"publication-title\">Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?<\/span><\/a>, EMBO Rep 6(6):584-589 <span style=\"color:#ddd; font-size:12px\">699<\/span><\/li><li>Kmun\u00edcek J, Hynkov\u00e1 K, Jedlicka T, Nagata Y, Negri A, Gago F, Wade RC, Damborsk\u00fd J (2005). <a href=\"https:\/\/doi.org\/10.1021\/bi047912o\"><span class=\"publication-title\">Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26<\/span><\/a>, Biochemistry 44(9):3390-3401 <span style=\"color:#ddd; font-size:12px\">701<\/span><\/li><li>Ehrlich LP, Nilges M, Wade RC (2005). <a href=\"https:\/\/doi.org\/10.1002\/prot.20272\"><span class=\"publication-title\">The Impact of Protein Flexibility on Protein-protein Docking<\/span><\/a>, Proteins 58(1):126-133 <span style=\"color:#ddd; font-size:12px\">703<\/span><\/li><li>McCammon J, Wade R (2005). <span class=\"publication-title\">Pushing the limits: Editorial Overview. Curr<\/span>, Opin. Struct. Biol. 15:135\u2013136 <span style=\"color:#ddd; font-size:12px\">751<\/span><\/li><li>Ulbrich S (2005). <span class=\"publication-title\">The Protein Structure Annotation Tool ProSAT2<\/span>, Studienarbeit <span style=\"color:#ddd; font-size:12px\">1026<\/span><\/li><\/ul><h2 id=\"publication-year-2004\">2004<\/h2><ul class=\"publications-list\"><li>Wade RC, Henrich S, Wang T (2004). <a href=\"https:\/\/doi.org\/10.1016\/j.ddtec.2004.11.018\"><span class=\"publication-title\">Using 3D protein structures to derive 3D-QSARs<\/span><\/a>, Drug Discovery Today: Technologies 1(3):241-246 <span style=\"color:#ddd; font-size:12px\">704<\/span><\/li><li>Schleinkofer K, Wiedemann U, Otte L, Wang T, Krause G, Oschkinat H, Wade RC (2004). <a href=\"https:\/\/doi.org\/10.1016\/j.jmb.2004.09.063\"><span class=\"publication-title\">Comparative Structural and Energetic Analysis of WW Domain-Peptide Interactions<\/span><\/a>, Journal of Molecular Biology 344(3):865-881 <span style=\"color:#ddd; font-size:12px\">705<\/span><\/li><li>Winn PJ, Religa TL, Battey JN, Banerjee A, Wade RC (2004). <a href=\"https:\/\/doi.org\/10.1016\/j.str.2004.06.017\"><span class=\"publication-title\">Determinants of Functionality in the Ubiquitin Conjugating Enzyme Family<\/span><\/a>, Structure 12(9):1563-1574 <span style=\"color:#ddd; font-size:12px\">706<\/span><\/li><li>Wang T, Tomic S, Gabdoulline RR, Wade RC (2004). <a href=\"https:\/\/doi.org\/10.1529\/biophysj.104.040964\"><span class=\"publication-title\">How Optimal are the Binding Energetics of Barnase and Barstar?<\/span><\/a>, Biophysical Journal 87(3):1618-1630 <span style=\"color:#ddd; font-size:12px\">707<\/span><\/li><li>Rienzo FD, Gabdoulline RR, Wade RC, Sola M, Menziani MC (2004). <a href=\"https:\/\/doi.org\/10.1007\/s00018-004-3181-5\"><span class=\"publication-title\">Computational approaches to structural and functional analysis of plastocyanin and other blue copper proteins<\/span><\/a>, Cellular and Molecular Life Sciences (CMLS) 61(10):1123-1142 <span style=\"color:#ddd; font-size:12px\">708<\/span><\/li><li>Wade RC, Winn PJ, Schlichting I, Sudarko  (2004). <a href=\"https:\/\/doi.org\/10.1016\/j.jinorgbio.2004.02.007\"><span class=\"publication-title\">A survey of active site access channels in cytochromes P450<\/span><\/a>, Journal of Inorganic Biochemistry 98(7):1175-1182 <span style=\"color:#ddd; font-size:12px\">709<\/span><\/li><li>Damborsky J, Kmunicek J, Jedlicka T, Luengo S, Gago F, Ortiz AR, Wade RC (2004). <span class=\"publication-title\">Rational Re-design of Haloalkane Dehalogenases Guided by Comparative Binding Energy Analysis<\/span>, In Enzyme functionality: Design, Engineering and Screening, pp. pp79\u201396, Ed. A. Svendsen, Marcel Dekker, New York <span style=\"color:#ddd; font-size:12px\">710<\/span><\/li><\/ul><h2 id=\"publication-year-2003\">2003<\/h2><ul class=\"publications-list\"><li>Zemojtel T, Wade RC, Dandekar T (2003). <a href=\"https:\/\/doi.org\/10.1016\/S0014-5793(03)01081-0\"><span class=\"publication-title\">In Search of the Prototype of Nitric Oxide Synthase<\/span><\/a>, FEBS Letters 554(1-2):1-5 <span style=\"color:#ddd; font-size:12px\">711<\/span><\/li><li>Ferrari S, Costi PM, Wade RC (2003). <a href=\"https:\/\/doi.org\/10.1016\/j.chembiol.2003.11.012\"><span class=\"publication-title\">Inhibitor specificity via protein dynamics: Insights from design of antibacterial agents targeted against thymidylate synthase<\/span><\/a>, Chemistry &#038; Biology 10(12):1183-1193 <span style=\"color:#ddd; font-size:12px\">712<\/span><\/li><li>Berto\u0161a B, Koji\u0107-Prodi\u0107 B, Wade RC, Ramek M, Piperaki S, Tsantili-Kakoulidou A, Tomi\u0107 S (2003). <a href=\"https:\/\/doi.org\/10.1021\/ci034063n\"><span class=\"publication-title\">A New Approach to Predict the Biological Activity of Molecules Based on Similarity of Their Interaction Fields and the logP and logD Values: Application to Auxins<\/span><\/a>, J. Chem. Inf. Comput. Sci. 43(5):1532-1541 <span style=\"color:#ddd; font-size:12px\">713<\/span><\/li><li>Essigke T, Ullmann GM, Wade RC (2003). <span class=\"publication-title\">What Determines the Redox Potential of Ferredoxins?<\/span>, In &#8222;Proceedings of the 13th International Conference on Cytochromes P450&#8220;, pp. 25\u201330, Monduzzi Editore, Bologna <span style=\"color:#ddd; font-size:12px\">714<\/span><\/li><li>Kmun\u00ed\u010dek J, Boh\u00e1\u010d M, Luengo S, Gago F, Wade RC, Damborsk\u00fd J (2003). <a href=\"https:\/\/doi.org\/10.1023\/A:1026159215220\"><span class=\"publication-title\">Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations<\/span><\/a>, J. Comput. Aided Mol. Des. 17:299\u2013311 <span style=\"color:#ddd; font-size:12px\">715<\/span><\/li><li>Gabdoulline R, Wade RC, Walther D (2003). <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkg588\"><span class=\"publication-title\">MolSurfer: a macromolecular interface navigator<\/span><\/a>, Nucleic Acids Research 31(13):3349-3351 <span style=\"color:#ddd; font-size:12px\">716<\/span><\/li><li>Gabdoulline RR, Kummer U, Olsen LF, Wade RC (2003). <a href=\"https:\/\/doi.org\/10.1016\/S0006-3495(03)74574-3\"><span class=\"publication-title\">Concerted Simulations Reveal How Peroxidase Compound III Formation Results in Cellular Oscillations<\/span><\/a>, Biophysical Journal 85(3):1421-1428 <span style=\"color:#ddd; font-size:12px\">717<\/span><\/li><li>Gabdoulline RR, Hoffmann R, Leitner F, Wade RC (2003). <a href=\"https:\/\/doi.org\/10.1093\/bioinformatics\/btg220\"><span class=\"publication-title\">ProSAT: Functional annotation of protein 3D structures<\/span><\/a>, Bioinformatics 19(13):1723-1725 <span style=\"color:#ddd; font-size:12px\">718<\/span><\/li><li>Finocchiaro G, Wang T, Hoffmann R, Gonzalez A, C. R (2003). <a href=\"https:\/\/doi.org\/10.1093\/nar\/gkg113\"><span class=\"publication-title\">DSMM &#8211; a Database of Simulated Molecular Motions<\/span><\/a>, Nucleic Acids Research 31(1):456-457 <span style=\"color:#ddd; font-size:12px\">719<\/span><\/li><li>Wang T, Wade RC (2003). <a href=\"https:\/\/doi.org\/10.1002\/prot.10248\"><span class=\"publication-title\">Implicit Solvent Models for Flexible Protein-protein Docking by Molecular Dynamics Simulation<\/span><\/a>, Proteins 50(1):158-169 <span style=\"color:#ddd; font-size:12px\">720<\/span><\/li><li>Essigke T, Ullmann M, Wade R (2003). <span class=\"publication-title\">Proceedings of the 13textsuperscriptth International Conference on Cytochromes P450<\/span>, In What Determines the Redox Potential of Ferredoxins?, pp. pp25\u201330, Monduzzi Editore, Bologna <span style=\"color:#ddd; font-size:12px\">752<\/span><\/li><\/ul><h2 id=\"publication-year-2002\">2002<\/h2><ul class=\"publications-list\"><li>Deprez E, Gill E, Helms V, Wade RC, Hoa GHB (2002). <a href=\"https:\/\/doi.org\/10.1016\/S0162-0134(02)00467-1\"><span class=\"publication-title\">Specific and Non-specific Effects of Potassium Cations on Substrate-protein Interactions in Cytocromes P450cam and P450lin<\/span><\/a>, Journal of Inorganic Biochemistry 91(4):597-606 <span style=\"color:#ddd; font-size:12px\">721<\/span><\/li><li>Wang T, Wade RC (2002). <a href=\"https:\/\/doi.org\/10.1021\/jm020900l\"><span class=\"publication-title\">Comparative Binding Energy (COMBINE) Analysis of OppA\u2212Peptide Complexes to Relate Structure to Binding Thermodynamics<\/span><\/a>, J. Med. Chem. 45(22):4828-4837 <span style=\"color:#ddd; font-size:12px\">722<\/span><\/li><li>Winn PJ, Ludemann SK, Gauges R, Lounnas V, Wade RC (2002). <a href=\"https:\/\/doi.org\/10.1073\/pnas.082522999\"><span class=\"publication-title\">Comparison of the dynamics of substrate access channels in three cytochrome P450s reveals different opening mechanisms and a new functional role for a buried arginine<\/span><\/a>, Proceedings of the National Academy of Sciences 99(8):5361-5366 <span style=\"color:#ddd; font-size:12px\">723<\/span><\/li><li>Gabdoulline RR, Wade RC (2002). <a href=\"https:\/\/doi.org\/10.1016\/S0959-440X(02)00311-1\"><span class=\"publication-title\">Biomolecular diffusional association<\/span><\/a>, Current Opinion in Structural Biology 12(2):204-213 <span style=\"color:#ddd; font-size:12px\">724<\/span><\/li><li>Banerjee A, Wade RC (2002). <a href=\"https:\/\/doi.org\/10.1002\/jmr.561\"><span class=\"publication-title\">Elusive recognition determinants for ubiquitination<\/span><\/a>, J. Mol. Recognit. 15(1):3-5 <span style=\"color:#ddd; font-size:12px\">725<\/span><\/li><li>Rienzo FD, Gabdoulline RR, Wade RC, Menziani MC (2002). <span class=\"publication-title\">Biologically relevant properties of copper-containing proteins analysed by means of semi-quantitative and quantitative theoretical descriptors<\/span>, In Handbook of Copper Pharmacology and Toxicology, pp. pp. 53\u201380, Ed. E. J. Massaro, Humana Press, Totowa, New Jersey <span style=\"color:#ddd; font-size:12px\">726<\/span><\/li><\/ul><h2 id=\"publication-year-2001\">2001<\/h2><ul class=\"publications-list\"><li>Rienzo FD, Gabdoulline RR, Menziani MC, Benedetti PGD, Wade RC (2001). <a href=\"https:\/\/doi.org\/10.1016\/S0006-3495(01)75947-4\"><span class=\"publication-title\">Electrostatic Analysis and Brownian Dynamics Simulation of the Association of Plastocyanin and Cytochrome F<\/span><\/a>, Biophysical Journal 81(6):3090-3104 <span style=\"color:#ddd; font-size:12px\">753<\/span><\/li><li>Kmun\u00edc\u030cek J, Luengo S, Gago F, Ortiz AR, Wade RC, Damborsk\u00fd J (2001). <a href=\"https:\/\/doi.org\/10.1021\/bi010464p\"><span class=\"publication-title\">Comparative Binding Energy (COMBINE) Analysis of the Substrate Specificity of Haloalkane Dehalogenase from Xanthobacter Autotrophicus GJ10<\/span><\/a>, Biochemistry 40(30):8905-8917 <span style=\"color:#ddd; font-size:12px\">754<\/span><\/li><li>Wang T, Wade RC (2001). <a href=\"https:\/\/doi.org\/10.1021\/jm001070j\"><span class=\"publication-title\">Comparative Binding Energy (COMBINE) analysis of Influenza Neuraminidase-Inhibitor Complexes<\/span><\/a>, J. Med. Chem. 44(6):961-971 <span style=\"color:#ddd; font-size:12px\">755<\/span><\/li><li>Gabdoulline RR, Wade RC (2001). <a href=\"https:\/\/doi.org\/10.1006\/jmbi.2000.4404\"><span class=\"publication-title\">Protein-protein Association: Investigation of Factors Influencing Association Rates by Brownian Dynamics Simulations<\/span><\/a>, Journal of Molecular Biology 306(5):1139-1155 <span style=\"color:#ddd; font-size:12px\">756<\/span><\/li><li>Luedemann S, Gabdoulline R, Lounnas V, Wade R (2001). <a href=\"https:\/\/projects.h-its.org\/mcm\/abs\/lglw_2001_1.html\"><span class=\"publication-title\">Substrate access to cytochrome P450cam investigated by molecular dynamics simulations: An interactive look at the underlying mechanisms<\/span><\/a>, Internet. J. Chem., 4, 6 <span style=\"color:#ddd; font-size:12px\">757<\/span><\/li><li>Wade RC, Gabdoulline RR, Rienzo FD (2001). <a href=\"https:\/\/doi.org\/10.1002\/qua.1204\"><span class=\"publication-title\">Protein Interaction Property Similarity Analysis<\/span><\/a>, Int. J. Quantum Chem. 83(3-4):122-127 <span style=\"color:#ddd; font-size:12px\">758<\/span><\/li><li>Tomic S, Wade R (2001). <span class=\"publication-title\">COMBINE Analysis of Nuclear Receptor-DNA Binding Specificity: Comparison of Two Data Sets<\/span>, Croat. Chem. Acta. 74:295\u2013314 <span style=\"color:#ddd; font-size:12px\">759<\/span><\/li><li>Ehrlich LP, Wade RC (2001). <a href=\"https:\/\/doi.org\/10.1002\/0471224413.ch2\"><span class=\"publication-title\">Protein-Protein Docking<\/span><\/a>, Reviews in Computational Chemistry,pp.61-97,John Wiley &#038; Sons, Inc. <span style=\"color:#ddd; font-size:12px\">760<\/span><\/li><li>Jalkanen K, Nieminen R, Frimand K, Bohr J, Bohr H, Wade R, Tajkhorshid E, Suhai S (2001). <a href=\"https:\/\/doi.org\/10.1016\/S0301-0104(01)00267-1\"><span class=\"publication-title\">A Comparison of Aqueous Solvent Models Used in the Calculation of the Raman and ROA spectra of L-alanine<\/span><\/a>, Chemical Physics 265(2):125-151 <span style=\"color:#ddd; font-size:12px\">761<\/span><\/li><li>Wang T, Wade R (2001). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/ww_2001_2.html\"><span class=\"publication-title\">COMBINE 3D-QSAR analysis of Influenza Neuraminidase Inhibitors<\/span><\/a>, In Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships, pp. pp78\u201382, Eds. Holtje, H-D., Sippl,W., Prous Science S.A., Barcelona <span style=\"color:#ddd; font-size:12px\">762<\/span><\/li><li>Wade R (2001). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/w_2001_1.html\"><span class=\"publication-title\">Derivation of QSARs using 3D Structural Models of Protein-ligand complexes by COMBINE Analysis<\/span><\/a>, In Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships, pp. pp23\u201328, Eds. Holtje, H-D., Sippl,W., Prous Science S.A., Barcelona <span style=\"color:#ddd; font-size:12px\">763<\/span><\/li><\/ul><h2 id=\"publication-year-2000\">2000<\/h2><ul class=\"publications-list\"><li>Lamotte-Brasseur J, Dubus A, Wade RC (2000). <a href=\"https:\/\/doi.org\/10.1002\/(SICI)1097-0134(20000701)40:1<23::AID-PROT40>3.0.CO;2-7&#8243;><span class=\"publication-title\">pKa calculations for class C beta-lactamases: The role of tyr-150<\/span><\/a>, Proteins 40:23\u201328 <span style=\"color:#ddd; font-size:12px\">769<\/span><\/li><li>L\u00fcdemann SK, Lounnas V, Wade RC (2000). <a href=\"https:\/\/doi.org\/10.1006\/jmbi.2000.4154\"><span class=\"publication-title\">How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics to investigate ligand access channels and mechanisms<\/span><\/a>, Journal of Molecular Biology 303(5):797-811 <span style=\"color:#ddd; font-size:12px\">764<\/span><\/li><li>L\u00fcdemann SK, Lounnas V, Wade RC (2000). <a href=\"https:\/\/doi.org\/10.1006\/jmbi.2000.4155\"><span class=\"publication-title\">How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways<\/span><\/a>, Journal of Molecular Biology 303(5):813-830 <span style=\"color:#ddd; font-size:12px\">765<\/span><\/li><li>Das B, Helms V, Lounnas V, Wade RC (2000). <a href=\"https:\/\/doi.org\/10.1016\/S0162-0134(00)00095-7\"><span class=\"publication-title\">Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam<\/span><\/a>, Journal of Inorganic Biochemistry 81(3):121-131 <span style=\"color:#ddd; font-size:12px\">766<\/span><\/li><li>Rienzo FD, Gabdoulline R, Menziani MC, Wade R (2000). <a href=\"https:\/\/doi.org\/10.1110\/ps.9.8.1439\"><span class=\"publication-title\">Blue Copper Proteins: A Comparative Analysis of their Molecular Interaction Properties<\/span><\/a>, Protein Sci. 9(8):1439-1454 <span style=\"color:#ddd; font-size:12px\">767<\/span><\/li><li>Nardi F, Kemmink J, Sattler M, Wade RC (2000). <a href=\"https:\/\/doi.org\/10.1023\/A:1008380807603\"><span class=\"publication-title\">The cisProline(i-1)-Aromatic(i) Interaction: Folding of the Ala-cisPro-Tyr peptide characterized by NMR and theoretical approaches<\/span><\/a>, J. Biomol. NMR 17:63\u201377 <span style=\"color:#ddd; font-size:12px\">768<\/span><\/li><li>Tomic S, Nilsson L, Wade RC (2000). <a href=\"https:\/\/doi.org\/10.1021\/jm9911175\"><span class=\"publication-title\">Nuclear receptor-DNA binding specificity: a COMBINE and Free-Wilson QSAR analysis<\/span><\/a>, J. Med. Chem. 43(9):1780-1792 <span style=\"color:#ddd; font-size:12px\">770<\/span><\/li><li>Tomi\u0107 S, Nilsson L, Wade RC (2000). <a href=\"https:\/\/doi.org\/10.1007\/978-1-4615-4141-7_35\"><span class=\"publication-title\">COMBINE and Free-Wilson QSAR analysis of nuclear receptor &#8211; DNA binding<\/span><\/a>, Molecular Modeling and Prediction of Bioactivity,pp.269-270,Springer US <span style=\"color:#ddd; font-size:12px\">771<\/span><\/li><\/ul><h2 id=\"publication-year-1999\">1999<\/h2><ul class=\"publications-list\"><li>Blomberg N, Gabdoulline RR, Nilges M, Wade RC (1999). <a href=\"https:\/\/doi.org\/10.1002\/(SICI)1097-0134(19991115)37:3<379::AID-PROT6>3.0.CO;2-K&#8220;><span class=\"publication-title\">Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity<\/span><\/a>, Proteins 37(3):379-387 <span style=\"color:#ddd; font-size:12px\">937<\/span><\/li><li>Gabdoulline RR, Wade RC (1999). <a href=\"https:\/\/doi.org\/10.1002\/(SICI)1099-1352(199907\/08)12:4<226::AID-JMR462>3.0.CO;2-P&#8220;><span class=\"publication-title\">On the protein-protein diffusional encounter complex<\/span><\/a>, J. Mol. Recognit. 12(4):226-234 <span style=\"color:#ddd; font-size:12px\">938<\/span><\/li><li>Gabdoulline R, Wade R, Walter D (1999). <a href=\"https:\/\/projects.h-its.org\/dbase\/molsurfer\/doc\/tibs.html\"><span class=\"publication-title\">MolSurfer: 2D maps to navigate 3D structures of proteins and their complexes<\/span><\/a>, Trends in Biochem. Sci. 24:285\u2013287 <span style=\"color:#ddd; font-size:12px\">772<\/span><\/li><li>Nielsen JE, Andersen KV, Honig B, Hooft RWW, Klebe G, Vriend G, Wade RC (1999). <a href=\"https:\/\/doi.org\/10.1093\/protein\/12.8.657\"><span class=\"publication-title\">Improving macromolecular electrostatics calculations<\/span><\/a>, Protein Engineering, Design and Selection 12(8):657-662 <span style=\"color:#ddd; font-size:12px\">774<\/span><\/li><li>Elcock AH, Gabdoulline RR, Wade RC, McCammon J (1999). <a href=\"https:\/\/doi.org\/10.1006\/jmbi.1999.2919\"><span class=\"publication-title\">Computer Simulation of Protein-Protein Association Kinetics: Acetylcholinesterase-Fasciculin<\/span><\/a>, Journal of Molecular Biology 291(1):149-162 <span style=\"color:#ddd; font-size:12px\">775<\/span><\/li><li>Ibragimova GT, Wade RC (1999). <a href=\"https:\/\/doi.org\/10.1016\/S0006-3495(99)77059-1\"><span class=\"publication-title\">Stability of the beta-sheet of the WW domain: A Molecular Dynamics Simulation Study<\/span><\/a>, Biophysical Journal 77(4):2191-2198 <span style=\"color:#ddd; font-size:12px\">777<\/span><\/li><li>Bitomsky W, Wade RC (1999). <a href=\"https:\/\/doi.org\/10.1021\/ja983319g\"><span class=\"publication-title\">Docking of Glycosaminoglycans to Heparin-binding Proteins: Validation for aFGF, bFGF and Antithrombin and Application to IL-8<\/span><\/a>, J. Am. Chem. Soc. 121(13):3004-3013 <span style=\"color:#ddd; font-size:12px\">778<\/span><\/li><li>Lounnas V, L\u00fcdemann SK, Wade RC (1999). <a href=\"https:\/\/doi.org\/10.1016\/S0301-4622(98)00237-3\"><span class=\"publication-title\">Towards molecular dynamics simulations of large proteins with a hydration shell at constant presssure<\/span><\/a>, Biophysical Chemistry 78(1-2):157-182 <span style=\"color:#ddd; font-size:12px\">779<\/span><\/li><li>Lamotte-Brasseur J, Lounnas V, Raquet X, Wade RC (1999). <a href=\"https:\/\/doi.org\/10.1110\/ps.8.2.404\"><span class=\"publication-title\">pKa calculations for class A beta-lactamases: influence of substrate binding<\/span><\/a>, Protein Science 8(2):404-409 <span style=\"color:#ddd; font-size:12px\">780<\/span><\/li><li>Nardi F, Wade R (1999). <a href=\"https:\/\/www.elsevier.com\/books\/molecular-dynamics\/balbuena\/978-0-444-82910-8\"><span class=\"publication-title\">Ways and Means to Enhance the Configurational Sampling of Small Peptides in Aqueous Solution in Molecular Dynamics Simulations<\/span><\/a>, In Theoretical and Computational Chemistry Book Series, vol. 7, pp. Ch. 21, 859\u2013898, Eds. Balbuena,P.B. and Seminario,J.M., Elsevier Science: Amsterdam, Netherlands <span style=\"color:#ddd; font-size:12px\">781<\/span><\/li><li>Knapp-Mohammady M, Jalkanen K, Nardi F, Wade R, Suhai S (1999). <a href=\"https:\/\/doi.org\/10.1016\/S0301-0104(98)00387-5\"><span class=\"publication-title\">L-Alanyl-L-alanine in the zwitterionic state: structures determined in the presence of explicit water molecules and with continuum models using density functional theory<\/span><\/a>, Chemical Physics 240(1-2):63-77 <span style=\"color:#ddd; font-size:12px\">782<\/span><\/li><li>Linge JP, Nilges M, Ehrlich L (1999). <a href=\"https:\/\/doi.org\/10.1023\/A:1008347330165\"><span class=\"publication-title\">StarDOM: From STAR format to XML<\/span><\/a>, Journal of Biomolecular NMR,15(2):169-172 <span style=\"color:#ddd; font-size:12px\">942<\/span><\/li><\/ul><h2 id=\"publication-year-1998\">1998<\/h2><ul class=\"publications-list\"><li>Helms V, Wade RC (1998). <a href=\"https:\/\/doi.org\/10.1002\/(SICI)1097-0134(19980815)32:3<381::AID-PROT12>3.0.CO;2-5&#8243;><span class=\"publication-title\">Hydration energy landscape of the active site cavity in cytochrome P450cam<\/span><\/a>, Proteins 32(3):381-396 <span style=\"color:#ddd; font-size:12px\">939<\/span><\/li><li>Wade RC, Gabdoulline RR, Luty BA (1998). <a href=\"https:\/\/doi.org\/10.1002\/(SICI)1097-0134(19980601)31:4<406::AID-PROT7>3.0.CO;2-F&#8220;><span class=\"publication-title\">Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases<\/span><\/a>, Proteins 31(4):406-416 <span style=\"color:#ddd; font-size:12px\">940<\/span><\/li><li>Gabdoulline RR, Wade RC (1998). <a href=\"https:\/\/doi.org\/10.1006\/meth.1998.0588\"><span class=\"publication-title\">Brownian Dynamics Simulation of Protein\u2013Protein Diffusional Encounter<\/span><\/a>, Methods 14(3):329-341 <span style=\"color:#ddd; font-size:12px\">795<\/span><\/li><li>Ringrose L, Lounnas V, Ehrlich L, Buchholz F, Wade R, Stewart A (1998). <a href=\"https:\/\/doi.org\/10.1006\/jmbi.1998.2149\"><span class=\"publication-title\">Comparative Kinetic Analysis of FLP and Cre Recombinases: Mathematical Models for DNA Binding and Recombination<\/span><\/a>, Journal of Molecular Biology 284(2):363-384 <span style=\"color:#ddd; font-size:12px\">783<\/span><\/li><li>Worth GA, Nardi F, Wade RC (1998). <a href=\"https:\/\/doi.org\/10.1021\/jp9808532\"><span class=\"publication-title\">Use of Multiple Molecular Dynamics Trajectories to Study Biomolecules in Solution: The YTGP Peptide<\/span><\/a>, J. Phys. Chem. B 102(32):6260-6272 <span style=\"color:#ddd; font-size:12px\">784<\/span><\/li><li>Wade RC, Gabdoulline RR, Ludemann SK, Lounnas V (1998). <a href=\"https:\/\/doi.org\/10.1073\/pnas.95.11.5942\"><span class=\"publication-title\">Electrostatic steering and ionic tethering in enzyme-ligand binding: Insights from simulations<\/span><\/a>, Proceedings of the National Academy of Sciences 95(11):5942-5949 <span style=\"color:#ddd; font-size:12px\">785<\/span><\/li><li>Tomic S, Gabdoulline R, Kojic-Prodic B, Wade R (1998). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/ijc_98.html\"><span class=\"publication-title\">Classification of auxin related compounds based on similarity of their interaction fields: Extension to a new set of compounds<\/span><\/a>, Internet J. Chem. 1:26 <span style=\"color:#ddd; font-size:12px\">786<\/span><\/li><li>Ibragimova GT, Wade RC (1998). <a href=\"https:\/\/doi.org\/10.1016\/S0006-3495(98)77997-4\"><span class=\"publication-title\">Importance of explicit salt ions for protein stability in molecular dynamics simulation<\/span><\/a>, Biophysical Journal 74(6):2906-2911 <span style=\"color:#ddd; font-size:12px\">787<\/span><\/li><li>Helms V, Wade RC (1998). <a href=\"https:\/\/doi.org\/10.1021\/ja9738539\"><span class=\"publication-title\">Computational Alchemy to Calculate Absolute Protein-Ligand Binding Free Energy<\/span><\/a>, J. Am. Chem. Soc. 120(12):2710-2713 <span style=\"color:#ddd; font-size:12px\">788<\/span><\/li><li>Madura JD, Briggs JM, Wade RC, Gabdoulline RR (1998). <a href=\"https:\/\/doi.org\/10.1002\/0470845015.cba003\"><span class=\"publication-title\">Brownian Dynamics<\/span><\/a>, John Wiley &#038; Sons, Ltd <span style=\"color:#ddd; font-size:12px\">792<\/span><\/li><li>Tomi\u0107 S, Gabdoulline RR, Koji\u0107-Prodi\u0107 B, Wade RC (1998). <a href=\"https:\/\/doi.org\/10.1023\/A:1007973008558\"><span class=\"publication-title\">Classification of auxin plant hormones by interaction property similarity indices<\/span><\/a>, J. Comput. Aided Mol. Des. 12:63\u201379 <span style=\"color:#ddd; font-size:12px\">793<\/span><\/li><li>Ehrlich L, Reczko M, Bohr H, Wade RC (1998). <a href=\"https:\/\/doi.org\/10.1093\/protein\/11.1.11\"><span class=\"publication-title\">Prediction of protein hydration sites from sequence by modular neural networks<\/span><\/a>, Protein Engineering Design and Selection 11(1):11-19 <span style=\"color:#ddd; font-size:12px\">794<\/span><\/li><li>Wade RC, L\u00fcdemann S (1998). <a href=\"https:\/\/doi.org\/10.1007\/978-94-015-9028-0_4\"><span class=\"publication-title\">Computational Strategies for Modeling Receptor Flexibility in Studies of Receptor-Ligand Interactions<\/span><\/a>, Structure-Based Drug Design,pp.41-52,Springer Netherlands <span style=\"color:#ddd; font-size:12px\">796<\/span><\/li><li>Wade RC, Sobolev V, Ortiz AR, Peters G (1998). <a href=\"https:\/\/doi.org\/10.1007\/978-94-015-9028-0_19\"><span class=\"publication-title\">Computational Approaches to Modeling Receptor Flexibility Upon Ligand Binding: Application to Interfacially Activated Enzymes<\/span><\/a>, Structure-Based Drug Design,pp.223-232,Springer Netherlands <span style=\"color:#ddd; font-size:12px\">797<\/span><\/li><li>Wade RC, Ortiz AR, Gago F (1998). <a href=\"https:\/\/doi.org\/10.1023\/A:1027247618908\"><span class=\"publication-title\">Comparative binding energy analysis<\/span><\/a>, Perspectives in Drug Discovery and Design, 9:19-34 <span style=\"color:#ddd; font-size:12px\">943<\/span><\/li><\/ul><h2 id=\"publication-year-1997\">1997<\/h2><ul class=\"publications-list\"><li>Helms V, Wade RC (1997). <a href=\"https:\/\/doi.org\/10.1002\/(SICI)1096-987X(199703)18:4<449::AID-JCC1>3.0.CO;2-T&#8220;><span class=\"publication-title\">Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy<\/span><\/a>, J. Comput. Chem. 18(4):449-462 <span style=\"color:#ddd; font-size:12px\">941<\/span><\/li><li>Wade RC (1997). <a href=\"https:\/\/doi.org\/10.1016\/S0969-2126(97)00265-7\"><span class=\"publication-title\">\u2019Flu\u2019 and Structure Based Drug Design<\/span><\/a>, Structure 5(9):1139-1145 <span style=\"color:#ddd; font-size:12px\">798<\/span><\/li><li>Raquet X, Lounnas V, Lamotte-Brasseur J, Fr\u00e8re J, Wade R (1997). <a href=\"https:\/\/doi.org\/10.1016\/S0006-3495(97)78270-5\"><span class=\"publication-title\">pKa Calculations for Class A Beta-lactamases: Methodological and Mechanistic Implications<\/span><\/a>, Biophysical Journal 73(5):2416-2426 <span style=\"color:#ddd; font-size:12px\">799<\/span><\/li><li>L\u00fcdemann SK, Carugo O, Wade RC (1997). <a href=\"https:\/\/doi.org\/10.1007\/s008940050053\"><span class=\"publication-title\">Substrate Access to Cytochrome P450cam: a Comparison of a Thermal Motion Pathway Analysis with Molecular Dynamics Simulation Data<\/span><\/a>, Journal of Molecular Modeling 3(8):369-374 <span style=\"color:#ddd; font-size:12px\">801<\/span><\/li><li>Nardi F, Worth GA, Wade RC (1997). <a href=\"https:\/\/doi.org\/10.1016\/S1359-0278(97)00066-7\"><span class=\"publication-title\">Local interactions of aromatic residues in short peptides in aqueous solution: a combined database and energetic analysis<\/span><\/a>, Folding and Design 2:S62-S68 <span style=\"color:#ddd; font-size:12px\">802<\/span><\/li><li>Lounnas V, Wade RC (1997). <a href=\"https:\/\/doi.org\/10.1021\/bi9622940\"><span class=\"publication-title\">Exceptionally stable salt-bridges in cytochrome P450cam have functional roles<\/span><\/a>, Biochemistry 36(18):5402-5417 <span style=\"color:#ddd; font-size:12px\">803<\/span><\/li><li>Gabdoulline R, Wade R (1997). <a href=\"https:\/\/doi.org\/10.1016\/S0006-3495(97)78838-6\"><span class=\"publication-title\">Simulation of the Diffusional Association of Barnase and Barstar<\/span><\/a>, Biophysical Journal 72(5):1917-1929 <span style=\"color:#ddd; font-size:12px\">804<\/span><\/li><li>Ortiz AR, Pastor M, Palomer A, Cruciani G, Gago F, Wade RC (1997). <a href=\"https:\/\/doi.org\/10.1021\/jm9601617\"><span class=\"publication-title\">Reliability of CoMFA Models: Effects of Data Scaling and Variable Selection Using a Set of Human Synovial Fluid Phospholipase A2 Inhibitors<\/span><\/a>, J. Med. Chem. 40(7):1136-1148 <span style=\"color:#ddd; font-size:12px\">805<\/span><\/li><li>Helms V, Wade R (1997). <span class=\"publication-title\">Free energies of hydration from thermodynamic integration: A comparison of molecular mechanics force fields and evaluation of calculations accuracy<\/span>, J. Comp. Chem. 18:449\u2013462 <span style=\"color:#ddd; font-size:12px\">806<\/span><\/li><\/ul><h2 id=\"publication-year-1996\">1996<\/h2><ul class=\"publications-list\"><li>Sobolev V, Wade R, Vriend G, Edelman M (1996). <a href=\"https:\/\/doi.org\/10.1002\/(SICI)1097-0134(199605)25:1<120::AID-PROT10>3.0.CO;2-M&#8220;><span class=\"publication-title\">Molecular Docking Using Surface Complementarity<\/span><\/a>, Proteins 25:120-129 <span style=\"color:#ddd; font-size:12px\">814<\/span><\/li><li>Gabdoulline R, Wade R (1996). <a href=\"https:\/\/doi.org\/10.1016\/S0263-7855(97)00008-8\"><span class=\"publication-title\">Analytically defined surfaces to analyze molecular interaction properties<\/span><\/a>, Journal of Molecular Graphics 14(6):341-353 <span style=\"color:#ddd; font-size:12px\">807<\/span><\/li><li>Demchuk E, Wade RC (1996). <a href=\"https:\/\/doi.org\/10.1021\/jp960111d\"><span class=\"publication-title\">Improving the Continuum Dielectric Approach to Calculating pKas of Ionizable Groups in Proteins<\/span><\/a>, J. Phys. Chem. 100(43):17373-17387 <span style=\"color:#ddd; font-size:12px\">808<\/span><\/li><li>Wade R, Oschkinat H (1996). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/22.html\"><span class=\"publication-title\">Influence of glycosylation on the activity of rG-CSFs: in vitro studies: molecular structure and modeling<\/span><\/a>, Intl. J. Hematology 64:Suppl. 2, S1-S2, S7-S8 <span style=\"color:#ddd; font-size:12px\">809<\/span><\/li><li>Schulze H, Hoa GHB, Helms V, Wade RC, Jung C (1996). <a href=\"https:\/\/doi.org\/10.1021\/bi9527303\"><span class=\"publication-title\">Structural Changes in cytochrome P-450cam effected by the binding of the enantiomers (1R)-Camphor and (1S)-Camphor<\/span><\/a>, Biochemistry 35(45):14127-14138 <span style=\"color:#ddd; font-size:12px\">810<\/span><\/li><li>Wade R, Lounnas V, Helms V, Hoa GHB, Primo CD, Deprez E, Barret C, Kozin S, Jung C, Schulze H, Contzen J, Mouro C, Gill E, Simonneaux G, Bondon A, LeGrand N, Schlichting I (1996). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/video.html\"><span class=\"publication-title\">Fundamentals of Enzyme-Ligand Interactions in Cytochrome P450cam<\/span><\/a>, p. 3, Ed. M.J. Geisow, BIODIGM, Nottingham <span style=\"color:#ddd; font-size:12px\">811<\/span><\/li><li>Worth GA, Lecuyer C, Wade RC (1996). <a href=\"https:\/\/doi.org\/10.1016\/S0263-7855(96)00059-8\"><span class=\"publication-title\">TRAJAN: A Tool to Analyze Trajectories from Molecular Simulations<\/span><\/a>, Journal of Molecular Graphics 14(3):173-182 <span style=\"color:#ddd; font-size:12px\">812<\/span><\/li><li>Peters G, Olsen O, Svendsen A, Wade R (1996). <a href=\"https:\/\/doi.org\/10.1016\/S0006-3495(96)79207-X\"><span class=\"publication-title\">Theoretical investigation of the dynamics of the Active Site Lid in Rhizomucor Miehei Lipase<\/span><\/a>, Biophysical Journal 71(1):119-129 <span style=\"color:#ddd; font-size:12px\">813<\/span><\/li><li>Gabdoulline RR, Wade RC (1996). <a href=\"https:\/\/doi.org\/10.1021\/jp953109f\"><span class=\"publication-title\">Effective charges for Macromolecules in Solvent<\/span><\/a>, J. Phys. Chem. 100(9):3868-3878 <span style=\"color:#ddd; font-size:12px\">815<\/span><\/li><li>Helms V, Deprez E, Gill E, Barret C, Hoa GHB, Wade RC (1996). <a href=\"https:\/\/doi.org\/10.1021\/bi951817l\"><span class=\"publication-title\">Improved binding of cytochrome P450cam substrate analogues designed to fill extra space in the substrate binding pocket<\/span><\/a>, Biochemistry 35(5):1485-1499 <span style=\"color:#ddd; font-size:12px\">816<\/span><\/li><li>Wade RC (1996). <a href=\"https:\/\/doi.org\/10.1042\/bst0240254\"><span class=\"publication-title\">Brownian dynamics simulations of enzyme-substrate encounter<\/span><\/a>, Biochemical Society Transactions 24(1):254-259 <span style=\"color:#ddd; font-size:12px\">817<\/span><\/li><li>Reimer N, H\u00e4n\u00dfgen SU, Tichy WF (1996). <a href=\"https:\/\/doi.org\/10.1007\/BFb0030122\"><span class=\"publication-title\">Dynamically adapting the degree of parallelism with reflexive programs<\/span><\/a>, Parallel Algorithms for Irregularly Structured Problems 1117:313-318,Springer Berlin Heidelberg <span style=\"color:#ddd; font-size:12px\">851<\/span><\/li><\/ul><h2 id=\"publication-year-1995\">1995<\/h2><ul class=\"publications-list\"><li>Ortiz A, Pisabarro M, Gago F, Wade R (1995). <span class=\"publication-title\">Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis: Application to Human Synovial Fluid Phospholipase A2 Inhibitors<\/span>, In QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications, pp. pp439\u2013443, Eds. Sanz,F., Giraldo,J., Manaut,F, J.R. Prous Science Publishers, Barcelona <span style=\"color:#ddd; font-size:12px\">818<\/span><\/li><li>Worth GA, Wade RC (1995). <a href=\"https:\/\/doi.org\/10.1021\/j100048a025\"><span class=\"publication-title\">Aromatic &#8211; (i+2) Amine Interaction in Peptides<\/span><\/a>, J. Phys. Chem. 99(48):17473-17482 <span style=\"color:#ddd; font-size:12px\">819<\/span><\/li><li>Wade R (1995). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/8852332\"><span class=\"publication-title\">Simulation of enzyme-substrate interactions: the diffusional encounter step<\/span><\/a>, Acta Bioch. Polon. 42:419\u2013425 <span style=\"color:#ddd; font-size:12px\">820<\/span><\/li><li>Worth G, Wade R (1995). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/16.html\"><span class=\"publication-title\">Molecular Dynamics Study of Short Peptide Sequences from BPTI displaying aromatic-amide interactions<\/span><\/a>, In AIP Conference Proceedings  <span style=\"color:#ddd; font-size:12px\">821<\/span><\/li><li>Degenhardt M, Wade R (1995). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/jmm_95.html\"><span class=\"publication-title\">De novo design of ligands to block substrate access to cytochrome P450cam<\/span><\/a>, J. Mol. Model. 1:93 <span style=\"color:#ddd; font-size:12px\">822<\/span><\/li><li>Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, Ilin A, Antosiewicz J, Gilson MK, Bagheri B, Scott L, McCammon J (1995). <a href=\"https:\/\/doi.org\/10.1016\/0010-4655(95)00043-F\"><span class=\"publication-title\">Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program<\/span><\/a>, Computer Physics Communications 91(1-3):57-95 <span style=\"color:#ddd; font-size:12px\">823<\/span><\/li><li>Helms V, Wade R (1995). <a href=\"https:\/\/doi.org\/10.1016\/S0006-3495(95)79955-6\"><span class=\"publication-title\">Thermodynamics of Water Mediating Protein-Ligand Interactions in Cytochrome P450cam: A Molecular Dynamics Study<\/span><\/a>, Biophysical Journal 69(3):810-824 <span style=\"color:#ddd; font-size:12px\">824<\/span><\/li><li>Ortiz AR, Pisabarro MT, Gago F, Wade RC (1995). <a href=\"https:\/\/doi.org\/10.1021\/jm00014a020\"><span class=\"publication-title\">Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis<\/span><\/a>, J. Med. Chem. 38(14):2681-2691 <span style=\"color:#ddd; font-size:12px\">825<\/span><\/li><\/ul><h2 id=\"publication-year-1994\">1994<\/h2><ul class=\"publications-list\"><li>Madura JD, Davist ME, Gilson MK, Wades RC, Luty BA, McCammon JA (1994). <a href=\"https:\/\/doi.org\/10.1002\/9780470125823.ch4\"><span class=\"publication-title\">Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations<\/span><\/a>, Reviews in Computational Chemistry,pp.229-267,John Wiley &#038; Sons, Inc. <span style=\"color:#ddd; font-size:12px\">826<\/span><\/li><li>Pisabarro M, Palomer A, Ortiz A, Wade R, Gago F, Maule\u00f3n D, Carganico G (1994). <a href=\"https:\/\/doi.org\/10.1016\/0263-7855(94)80054-5\"><span class=\"publication-title\">Rational Drug Design: GRID- and LUDI-based Structural Modifications of a Human Synovial Fluid Phospholipase A2 Inhibitor Leading to Enhanced Activity.<\/span><\/a>, Journal of Molecular Graphics 12(1):72 <span style=\"color:#ddd; font-size:12px\">827<\/span><\/li><li>Wade RC, Luty BA, Demchuk E, Madura JD, Davis ME, Briggs JM, McCammon JA (1994). <a href=\"https:\/\/doi.org\/10.1038\/nsb0194-65\"><span class=\"publication-title\">Simulation of Enzyme-Substrate Encounter with Gated Active Sites<\/span><\/a>, Nat Struct Mol Biol 1(1):65-69 <span style=\"color:#ddd; font-size:12px\">828<\/span><\/li><li>Pisabarro MT, Ortiz AR, Palomer A, Cabre F, Garcia L, Wade RC, Gago F, Mauleon D, Carganico G (1994). <a href=\"https:\/\/doi.org\/10.1021\/jm00029a004\"><span class=\"publication-title\">Rational Modification of Human Synovial Fluid Phospholipase A2 Inhibitors<\/span><\/a>, J. Med. Chem. 37(3):337-341 <span style=\"color:#ddd; font-size:12px\">829<\/span><\/li><li>Demchuk E, Mueller T, Oschkinat H, Sebald W, Wade RC (1994). <a href=\"https:\/\/doi.org\/10.1002\/pro.5560030607\"><span class=\"publication-title\">Receptor binding properties of four-helix-bundle growth factors deduced from electrostatic analysis<\/span><\/a>, Protein Science 3(6):920-935 <span style=\"color:#ddd; font-size:12px\">830<\/span><\/li><li>Pisabarro MT, Ortiz AR, Serrano L, Wade RC (1994). <a href=\"https:\/\/doi.org\/10.1002\/prot.340200302\"><span class=\"publication-title\">Homology Modeling of the Abl-SH3 domain<\/span><\/a>, Proteins 20(3):203-215 <span style=\"color:#ddd; font-size:12px\">831<\/span><\/li><\/ul><h2 id=\"publication-year-1993\">1993<\/h2><ul class=\"publications-list\"><li>Luty BA, Wade RC, Madura JD, Davis ME, Briggs JM, McCammon JA (1993). <a href=\"https:\/\/doi.org\/10.1021\/j100103a040\"><span class=\"publication-title\">Brownian Dynamics Simulations of Diffusional Encounters between Triose Phosphate Isomerase and Glyceraldhyde Phosphate: Electrostatic Steering of Glyceraldehyde Phosphate<\/span><\/a>, J. Phys. Chem. 97(1):233-237 <span style=\"color:#ddd; font-size:12px\">832<\/span><\/li><li>Wade R, Davis M, Luty B, Madura J, McCammon J (1993). <a href=\"https:\/\/doi.org\/10.1016\/S0006-3495(93)81335-3\"><span class=\"publication-title\">Gating of the Active Site of Triose Phosphate Isomerase: Brownian Dynamics Simulations of Flexible Peptide Loops in the Enzyme<\/span><\/a>, Biophysical Journal 64(1):9-15 <span style=\"color:#ddd; font-size:12px\">833<\/span><\/li><li>Wade RC, Clark KJ, Goodford PJ (1993). <a href=\"https:\/\/doi.org\/10.1021\/jm00053a018\"><span class=\"publication-title\">Further Development of Hydrogen-Bond Functions for Use in Determining Energetically Favorable Binding Sites on Molecules of Known Structure. 1. Ligand Probe Groups with the Ability To Form Two Hydrogen Bonds<\/span><\/a>, J. Med. Chem. 36(1):140-147 <span style=\"color:#ddd; font-size:12px\">834<\/span><\/li><li>Wade RC, Goodford PJ (1993). <a href=\"https:\/\/doi.org\/10.1021\/jm00053a019\"><span class=\"publication-title\">Further Development of Hydrogen-Bond Functions for Use in Determining Energetically Favorable Binding Sites on Molecules of Known Structure. 2. Ligand Probe Groups with the Ability To Form More Than Two Hydrogen Bonds<\/span><\/a>, J. Med. Chem. 36(1):148-156 <span style=\"color:#ddd; font-size:12px\">835<\/span><\/li><li>Demchuk E, Vihinen M, Wade R, Korpela T (1993). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/6.html\"><span class=\"publication-title\">Modeling three-dimensional structure and electrostatics of alkali-stable cyclomaltodextrin glucanotransferase<\/span><\/a>, In Stability and Stabilization of Enzymes, pp. pp291\u2013298, Eds. van der Tweel,W.J.J.; Harder,A. and Buitelaar,R.M. Elsevier, Netherlands <span style=\"color:#ddd; font-size:12px\">836<\/span><\/li><li>Wade R, Bohr H, Wolynes P (1993). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/5.html\"><span class=\"publication-title\">Use of neural networks to predict hydration sites in proteins<\/span><\/a>, In Trends in QSAR and Molecular Modelling \u201992, pp. pp396\u2013397, Ed. Wermuth,C.G. ESCOM, Leiden <span style=\"color:#ddd; font-size:12px\">837<\/span><\/li><li>Wade R (1993). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/7.html\"><span class=\"publication-title\">Molecular Interaction Fields<\/span><\/a>, In 3D QSAR in Drug Design. Theory, Methods and Applications, pp. pp486\u2013505, Ed. Kubinyi,H. ESCOM, Leiden <span style=\"color:#ddd; font-size:12px\">838<\/span><\/li><\/ul><h2 id=\"publication-year-1992\">1992<\/h2><ul class=\"publications-list\"><li>Wade RC, McCammon J (1992). <a href=\"https:\/\/doi.org\/10.1016\/0022-2836(92)90394-Y\"><span class=\"publication-title\">Binding of an Antiviral Agent to a Sensitive and a Resistant Human Rhinovirus. Computer Simulations Studies with Sampling of Amino Acid Side-chain Conformations. I Mapping the Rotamers of Residue 188 of Viral Protein 1<\/span><\/a>, Journal of Molecular Biology 225(3):679-696 <span style=\"color:#ddd; font-size:12px\">839<\/span><\/li><li>Wade RC, McCammon J (1992). <a href=\"https:\/\/doi.org\/10.1016\/0022-2836(92)90395-Z\"><span class=\"publication-title\">Binding of an Antiviral Agent to a Sensitive and a Resistant Human Rhinovirus. Computer Simulations Studies with Sampling of Amino Acid Side-chain Conformations. II. Calculations of Free-energy Differences by Thermodynamic Integration<\/span><\/a>, Journal of Molecular Biology 225(3):697-712 <span style=\"color:#ddd; font-size:12px\">840<\/span><\/li><li>Wade RC, Bohr H, Wolynes PG (1992). <a href=\"https:\/\/doi.org\/10.1021\/ja00047a046\"><span class=\"publication-title\">Prediction of Water Binding Sites on Proteins by Neural Networks<\/span><\/a>, J. Am. Chem. Soc. 114(21):8284-8285 <span style=\"color:#ddd; font-size:12px\">841<\/span><\/li><\/ul><h2 id=\"publication-year-1991\">1991<\/h2><ul class=\"publications-list\"><li>Wade RC, Mazor MH, McCammon JA, Quiocho FA (1991). <a href=\"https:\/\/doi.org\/10.1002\/bip.360310802\"><span class=\"publication-title\">A Molecular Dynamics Study of Thermodynamic and Structural Aspects of the Hydration of Cavities in Proteins<\/span><\/a>, Biopolymers 31(8):919-931 <span style=\"color:#ddd; font-size:12px\">842<\/span><\/li><\/ul><h2 id=\"publication-year-1990\">1990<\/h2><ul class=\"publications-list\"><li>Wade R (1990). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/1990_1.html\"><span class=\"publication-title\">An Approach to the Design of Anti-Influenza Agents<\/span><\/a>, In Use of X-Ray Crystallography in the Design of Antiviral Agents, pp. pp61\u201374, Eds. Laver,G. and Air,G. Academic Press, Inc., San Diego <span style=\"color:#ddd; font-size:12px\">843<\/span><\/li><li>Wade RC (1990). <a href=\"https:\/\/doi.org\/10.1007\/BF00125318\"><span class=\"publication-title\">Solvation of the Active Site of Cytochrome P450-cam<\/span><\/a>, J Computer-Aided Mol Des 4(2):199-204 <span style=\"color:#ddd; font-size:12px\">844<\/span><\/li><li>Wade RC, Mazor MH, McCammon JA, Quiocho FA (1990). <a href=\"https:\/\/doi.org\/10.1021\/ja00175a048\"><span class=\"publication-title\">Hydration of Cavities in Proteins: a Molecular Dynamics Approach<\/span><\/a>, J. Am. Chem. Soc. 112(19):7057-7059 <span style=\"color:#ddd; font-size:12px\">845<\/span><\/li><\/ul><h2 id=\"publication-year-1989\">1989<\/h2><ul class=\"publications-list\"><li>Wade R, Goodford P (1989). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/2726808\"><span class=\"publication-title\">The Role of Hydrogen-bonds in Drug Binding<\/span><\/a>, In Prog. Clin. Biol. Res., pp. pp433\u2013444, Ed. Golombek,A., Alan R. Liss, Inc., New York <span style=\"color:#ddd; font-size:12px\">846<\/span><\/li><li>Boobbyer DNA, Goodford PJ, McWhinnie PM, Wade RC (1989). <a href=\"https:\/\/doi.org\/10.1021\/jm00125a025\"><span class=\"publication-title\">New Hydrogen-bond Potentials for Use in Determining Energetically Favourable Binding Sites on Molecules of Known Structure<\/span><\/a>, J. Med. Chem. 32(5):1083-1094 <span style=\"color:#ddd; font-size:12px\">847<\/span><\/li><li>Reynolds CA, Wade RC, Goodford PJ (1989). <a href=\"https:\/\/doi.org\/10.1016\/S0263-7855(89)80013-X\"><span class=\"publication-title\">Identifying Targets for Bioreductive Agents<\/span><\/a>, Journal of Molecular Graphics 7(2):103-108 <span style=\"color:#ddd; font-size:12px\">848<\/span><\/li><\/ul><h2 id=\"publication-year-1988\">1988<\/h2><ul class=\"publications-list\"><li>Wade R, Goodford P (1988). <a href=\"https:\/\/projects.villa-bosch.de\/mcm\/abs\/1988_1.html\"><span class=\"publication-title\">The Use of Molecular Graphics in the Design of Anti-influenza Agents<\/span><\/a>, Br. J. Pharmac. Proc. Suppl. 95:588P <span style=\"color:#ddd; font-size:12px\">849<\/span><\/li><\/ul>            <\/div>\n                                <div class=\"hits-tabs--tab\">\n              <\/ul><h2 id=\"publication-year-2025\">2025<\/h2><ul class=\"publications-list\"><li>Mu\u00f1iz\u2010Chicharro A (2025). <span class=\"publication-title\">Prediction of drug-protein binding kinetics (PhD Thesis)<\/span>, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">2057<\/span><\/li><li><span class=\"publication-title\">Prediction of Binding Kinetics of the Interleukin-13-Interleukin-13 Receptor alpha1 Complex (Master&#8217;s Thesis)<\/span>, Molecular Biosciences, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">2059<\/span><\/li><li>Herb N (2025). <a href=\"htmladdnormallink(HITS)http:\/\/www.h-its.org\"><span class=\"publication-title\">Prediction of Binding Kinetics of the Interleukin-13 \u2013 Interleukin-13 Receptor \u03b11 Complex (Master&#8217;s Thesis)<\/span><\/a>, htmladdnormallink(HITS)http:\/\/www.h-its.org <span style=\"color:#ddd; font-size:12px\">2232<\/span><\/li><li>Warken A (2025). <a href=\"htmladdnormallink(HITS)http:\/\/www.h-its.org\"><span class=\"publication-title\">Computational Investigation of Quinoline-Based Compounds and their Interaction with the Plasmodium Falciparum Drug Resistance Transporter (Bachelor&#8217;s Thesis)<\/span><\/a>, htmladdnormallink(HITS)http:\/\/www.h-its.org <span style=\"color:#ddd; font-size:12px\">2233<\/span><\/li><li>Tsengenes A (2025). <a href=\"htmladdnormallink(HITS)http:\/\/www.h-its.org\"><span class=\"publication-title\">Computer-Aided Drug Design of Small-Molecule Neurotrophin Mimetics (PhD Thesis)<\/span><\/a>, htmladdnormallink(HITS)http:\/\/www.h-its.org <span style=\"color:#ddd; font-size:12px\">2234<\/span><\/li><li>Fedorov R (2025). <a href=\"htmladdnormallink(HITS)http:\/\/www.h-its.org\"><span class=\"publication-title\">Machine Learning for Supported Organic Electrode Materials (PhD Thesis)<\/span><\/a>, htmladdnormallink(HITS)http:\/\/www.h-its.org <span style=\"color:#ddd; font-size:12px\">2235<\/span><\/li><\/ul><h2 id=\"publication-year-2024\">2024<\/h2><ul class=\"publications-list\"><li><span class=\"publication-title\">Structural bioinformatics approach to exploring transient binding pockets in proteins (Bachelor&#8217;s Thesis)<\/span>, Faculty of Biosciences and Faculty of Chemistry and Earth Sciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1899<\/span><\/li><li><span class=\"publication-title\">Structural bioinformatics approach to exploring transient binding pockets in proteins,\u00a0(Bachelor&#8217;s Thesis), Biochemistry, Faculty of Biosciences and Faculty of Chemistry and Earth Sciences, Ruprecht-Karls University, Heidelberg (Bachelor&#8217;s Thesis)<\/span> <span style=\"color:#ddd; font-size:12px\">1874<\/span><\/li><li><span class=\"publication-title\">Investigation of the impact of mutations in Cytochrome P450 reductase on the rate of electron transfer to Cytochrome P450 by molecular dynamics simulations (Master&#8217;s Thesis)<\/span>, Chemistry, Department of Chemistry, Ruprecht-Karls University, Heidelberg  <span style=\"color:#ddd; font-size:12px\">1898<\/span><\/li><\/ul><h2 id=\"publication-year-2023\">2023<\/h2><ul class=\"publications-list\"><li>Nie\u00dfner J (2023). <span class=\"publication-title\">Computational Models of Hen Egg White Lysozyme Physisorption to Silica- and Mica-like Surfaces (Master&#8217;s Thesis)<\/span>, Physics, Department of Physics and Astronomy, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1759<\/span><\/li><li>Athanasiou C (2023). <span class=\"publication-title\">Modeling of mechanistic effects of neurotrophin modulators (PhD Thesis)<\/span>, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1760<\/span><\/li><li>Tarnow M (2023). <span class=\"publication-title\">Optimization of a Drug: Polymer Formulation Exploiting a Computational Approach based on Molecular Dynamics Simulations (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Engineering Sciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1762<\/span><\/li><li>Ferraz M (2023). <span class=\"publication-title\">Enhanced sampling simulations and machine learning to address infectious diseases (PhD Thesis)<\/span>, Chemistry,  Department of Chemistry, Federal University of Pernambuco, Recife, Brazil <span style=\"color:#ddd; font-size:12px\">1785<\/span><\/li><\/ul><h2 id=\"publication-year-2022\">2022<\/h2><ul class=\"publications-list\"><li>Kaeser M (2022). <span class=\"publication-title\">Computational Investigation of the Structure Kinetics Relationship of Small-Molecule Compounds Binding the Histamine-1-Receptor (Master&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1582<\/span><\/li><li>Teuffel J (2022). <span class=\"publication-title\">Molecular Dynamics Simulation of a Mammalian Cytochrome P450 Protein and its Interaction with Substrates and Redox-Partners (Master&#8217;s Thesis)<\/span>, Biochemistry, Faculty of Biosciences and Faculty of Chemistry and Earth Sciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1445<\/span><\/li><li>Emmert M (2022). <span class=\"publication-title\">Generation and Testing of Boltzmann Generators Trained on Peptide Molecular Dynamics Simulations to Predict Peptide Conformational Behaviour (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1579<\/span><\/li><li>Hanke A (2022). <span class=\"publication-title\">P. falciparum Circumsporozoite protein epitope\/paratope interactions: Addressing the key role of molecular flexibility (Master&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1580<\/span><\/li><li>Cabezudo AC (2022). <span class=\"publication-title\">Structural Insights into Neurotrophin Receptor Dimerization using Coarse-grained Molecular Dynamics Simulations (Master&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1581<\/span><\/li><\/ul><h2 id=\"publication-year-2021\">2021<\/h2><ul class=\"publications-list\"><li>Dohrke J (2021). <span class=\"publication-title\">Molecular mechanisms of AMPAR modulation by auxiliary subunits (Master&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1207<\/span><\/li><li>Marinis PD (2021). <span class=\"publication-title\">Assessing ML-database augmentation approaches\r\n for Druggability Score calculations in TRAPP-pocket (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1441<\/span><\/li><li>Messner L (2021). <span class=\"publication-title\">Comparison of ligand docking to the AMPAR-TARP interaction site between different isoforms (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg, 2021 <span style=\"color:#ddd; font-size:12px\">1442<\/span><\/li><li>Han SB (2021). <span class=\"publication-title\">Multi-Resolution Simulation Study of CYP 2B4 to Investigate Complex Formation with Human NADPH-Cytochrome P450 Oxidoreductase in Lipid Bilayer (Master&#8217;s Thesis)<\/span>, Molecular Biosciences, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1443<\/span><\/li><li>De M (2021). <a href=\"https:\/\/archiv.ub.uni-heidelberg.de\/volltextserver\/30627\/\"><span class=\"publication-title\">The effects of the linker-DNA on linker histone positioning: a single-pair FRET study from mono to trichromatosomes (PhD Thesis)<\/span><\/a>, Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1444<\/span><\/li><\/ul><h2 id=\"publication-year-2020\">2020<\/h2><ul class=\"publications-list\"><li>Ormersbach F (2020). <span class=\"publication-title\">Computational ligand superimposition and analysis of protein-ligand interaction fingerprints (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1204<\/span><\/li><li>Jarosch L (2020). <span class=\"publication-title\">Computational modeling of SERCA interactions with S100A1ct and DWORF fingerprints (Bachelor&#8217;s Thesis)<\/span>, Biochemistry, Faculty of Biosciences and Faculty of Chemistry and Geosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1205<\/span><\/li><li>P\u00f6hner IA (2020). <a href=\"https:\/\/archiv.ub.uni-heidelberg.de\/volltextserver\/28399\/\"><span class=\"publication-title\">Computational approaches to drug design against the folate &amp; biopterin pathways of parasites causing neglected tropical diseases (PhD Thesis)<\/span><\/a>, Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1206<\/span><\/li><\/ul><h2 id=\"publication-year-2019\">2019<\/h2><ul class=\"publications-list\"><li>Hanke A (2019). <span class=\"publication-title\">Computational characterisation of protein homo- and heterodimer formation (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1010<\/span><\/li><li>Ullmann P (2019). <span class=\"publication-title\">Molecular dynamics simulation studies of gp41 cytoplasmic tail lateral embedding in phospholipid bilayer (Bachelor&#8217;s Thesis)<\/span>, Biosciences, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1011<\/span><\/li><li>Yuan J (2019). <span class=\"publication-title\">Druggability Assessment in TRAPP Procedure using Machine Learning Approaches (Master&#8217;s Thesis)<\/span>, Master of Scientific Computing, Fakult\u00e4t f\u00fcr Mathematik und Informatik, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1012<\/span><\/li><li>Ganotra GK (2019). <span class=\"publication-title\">Computational studies of drug-binding kinetics (PhD Thesis)<\/span>, Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1013<\/span><\/li><\/ul><h2 id=\"publication-year-2018\">2018<\/h2><ul class=\"publications-list\"><li>Friedrich P (2018). <span class=\"publication-title\">A novel method to treat gated protein-ligand binding via on-the-fly conformational updates within rigid body BD simulations (Master&#8217;s Thesis)<\/span>, Faculty of Physics, Ruprecht-Karls University Heidelberg <span style=\"color:#ddd; font-size:12px\">880<\/span><\/li><li>\u00d6ztuerk MA (2018). <span class=\"publication-title\">A computational approach to decipher chromatosome structure determinants (PhD Thesis)<\/span>, Combined Faculties of the Natural Sciences and for Mathematics, Ruprecht-Karls University Heidelberg <span style=\"color:#ddd; font-size:12px\">882<\/span><\/li><li>Dohrke J (2018). <span class=\"publication-title\">Modelling of Neurotrophin Receptors (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg <span style=\"color:#ddd; font-size:12px\">1032<\/span><\/li><\/ul><h2 id=\"publication-year-2017\">2017<\/h2><ul class=\"publications-list\"><li>Reinhardt M (2017). <span class=\"publication-title\">Development of Hydrodynamic Coarse-Grain Models for Brownian Dynamics Simulations of Crowded Protein Systems (Master&#8217;s Thesis)<\/span>, Faculty of Physics, Ruprecht-Karls University Heidelberg <span style=\"color:#ddd; font-size:12px\">877<\/span><\/li><li>Mustafa G (2017). <span class=\"publication-title\">Modeling and Simulation of Membrane Proteins to Understand their Structure, Dynamics and Function (PhD Thesis)<\/span>, Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University Heidelberg <span style=\"color:#ddd; font-size:12px\">878<\/span><\/li><li>Stank A (2017). <a href=\"https:\/\/doi.org\/10.11588\/heidok.00023095\"><span class=\"publication-title\">Computational Studies on the Relation Between Macromolecular Dynamics and Protein Binding and Function. (PhD Thesis)<\/span><\/a>, Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University Heidelberg <span style=\"color:#ddd; font-size:12px\">879<\/span><\/li><li>Buerkel C (2017). <span class=\"publication-title\">Towards development of Random Acceleration Molecular Dynamics simulation analysis software for predicting drug residence time (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg <span style=\"color:#ddd; font-size:12px\">1031<\/span><\/li><\/ul><h2 id=\"publication-year-2016\">2016<\/h2><ul class=\"publications-list\"><li>Ozboyaci M (2016). <span class=\"publication-title\">Modeling and Simulation of Protein-Surface Interactions (PhD Thesis)<\/span>, Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University Heidelberg <span style=\"color:#ddd; font-size:12px\">876<\/span><\/li><li>Stubbusch A (2016). <span class=\"publication-title\">Case Study of Human Growth Hormone Interactions by Brownian Dynamics Simulation (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg <span style=\"color:#ddd; font-size:12px\">1030<\/span><\/li><\/ul><h2 id=\"publication-year-2015\">2015<\/h2><ul class=\"publications-list\"><li>Berinski M (2015). <span class=\"publication-title\">Macromolecular Interactions: in silico prediction of the structures of complexes between proteins (PhD Thesis)<\/span>, Faculty of Informatics and Mathematics, Johann Wolfgang Goethe Universit\u00e4t, Frankfurt am Main <span style=\"color:#ddd; font-size:12px\">883<\/span><\/li><li>Ganotra GK (2015). <span class=\"publication-title\">Methods to Compute and Investigate Drug Binding Kinetics (Master&#8217;s Thesis)<\/span>, Life Science Informatics, University of Bonn <span style=\"color:#ddd; font-size:12px\">884<\/span><\/li><li>Yu X (2015). <span class=\"publication-title\">Multiscale Simulations of Cytochrome P450 Systems (PhD Thesis)<\/span>, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg <span style=\"color:#ddd; font-size:12px\">885<\/span><\/li><li>Horn M (2015). <span class=\"publication-title\">Clustering and Scoring the Druggability of Transient Protein Pockets (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg <span style=\"color:#ddd; font-size:12px\">1028<\/span><\/li><li>Waldhauer M (2015). <span class=\"publication-title\">Brownian Dynamics Simulations of Chymotrypsin Inhibitor 2 in Concentrated Protein Solutions (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg <span style=\"color:#ddd; font-size:12px\">1029<\/span><\/li><\/ul><h2 id=\"publication-year-2014\">2014<\/h2><ul class=\"publications-list\"><li>Tong R (2014). <span class=\"publication-title\">Comparative analysis of Adenylyl Cyclase binding sites (Bachelor&#8217;s Thesis)<\/span>, Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1027<\/span><\/li><\/ul><h2 id=\"publication-year-2013\">2013<\/h2><ul class=\"publications-list\"><li>Banerjee P (2013). <span class=\"publication-title\">An Algorithmic Approach to Peptidomimetics (Master&#8217;s Thesis)<\/span>, Masters Programme in Life Science Informatics, Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn <span style=\"color:#ddd; font-size:12px\">852<\/span><\/li><\/ul><h2 id=\"publication-year-2012\">2012<\/h2><ul class=\"publications-list\"><li>Monninger T (2012). <span class=\"publication-title\">Dynamische hybride Cloud f\u00fcr wissenschaftliche Anwendungen (Master&#8217;s Thesis)<\/span>, Fakultaet fuer Mathematik und Informatik, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">853<\/span><\/li><\/ul><h2 id=\"publication-year-2011\">2011<\/h2><ul class=\"publications-list\"><li>Subramaniam SR (2011). <span class=\"publication-title\">Sequence, Structure and Stability of Collagen and its Interaction with Collagenase. (PhD Thesis)<\/span>, University of Madras, Chennai.   <span style=\"color:#ddd; font-size:12px\">854<\/span><\/li><li>Garg D (2011). <span class=\"publication-title\">Computational and NMR Studies of Thymidylate Synthase and its Regulation (PhD Thesis)<\/span>, Faculty of Chemistry, Technical University of Munich <span style=\"color:#ddd; font-size:12px\">855<\/span><\/li><li>Veith N (2011). <span class=\"publication-title\">Structural Comparison of Pyruvate Kinases. (Master&#8217;s Thesis)<\/span>, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg <span style=\"color:#ddd; font-size:12px\">856<\/span><\/li><li>Nerini E (2011). <span class=\"publication-title\">System Approach to the Identification of Folate-related Enzyme Inhibitors with Anti-infectious Action (PhD Thesis)<\/span>, Doctoral School of Science and Technologies for Health Products, University of Modena and Reggio Emilia <span style=\"color:#ddd; font-size:12px\">857<\/span><\/li><\/ul><h2 id=\"publication-year-2010\">2010<\/h2><ul class=\"publications-list\"><li>Feldman-Salit A (2010). <span class=\"publication-title\">Computation and Modeling of Molecular Recognition: The Cysteine Synthase Complex (PhD Thesis)<\/span>, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg <span style=\"color:#ddd; font-size:12px\">858<\/span><\/li><\/ul><h2 id=\"publication-year-2009\">2009<\/h2><ul class=\"publications-list\"><li>Pachov GV (2009). <span class=\"publication-title\">Linker Histone-Nucleosome Interactions: A Modelling and Simulation Study (PhD Thesis)<\/span>, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University,Heidelberg <span style=\"color:#ddd; font-size:12px\">859<\/span><\/li><li>Berynskyy M (2009). <span class=\"publication-title\">Automatisierte Analyse von Brownian Dynamics Simulationen (Master&#8217;s Thesis)<\/span>, Bioinformatics, Giessen-Friedberg University of Applied Sciences <span style=\"color:#ddd; font-size:12px\">860<\/span><\/li><\/ul><h2 id=\"publication-year-2007\">2007<\/h2><ul class=\"publications-list\"><li>Motiejunas D (2007). <span class=\"publication-title\">Modeling of macromolecular interactions (PhD Thesis)<\/span>, Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University, Heidelberg <span style=\"color:#ddd; font-size:12px\">861<\/span><\/li><\/ul><h2 id=\"publication-year-2006\">2006<\/h2><ul class=\"publications-list\"><li>Zahran M (2006). <span class=\"publication-title\">Analyse a haut debit des proprietes electrostatiques des proteines de la famille des ubiquitines (High-throughput analysis of the electrostatic properties of proteins of the ubiquitin family) (Master&#8217;s Thesis)<\/span>, Bioinformatics, University Paris VII <span style=\"color:#ddd; font-size:12px\">862<\/span><\/li><\/ul><h2 id=\"publication-year-2005\">2005<\/h2><ul class=\"publications-list\"><li>Besson B (2005). <span class=\"publication-title\">Development of a software to aid the search of protein structural information to estimate kinetic parameters in systems biology applications (Master&#8217;s Thesis)<\/span>, Bioinformatics and Modeling, National Institute of Applied Science (INSA) Lyon <span style=\"color:#ddd; font-size:12px\">863<\/span><\/li><li>Johann TI (2005). <span class=\"publication-title\">Perturbation Methods in Molecular Dynamics Simulations with Implicit Solvent Models (Diploma Thesis)<\/span>, Physics, Ruperto-Carola University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1014<\/span><\/li><\/ul><h2 id=\"publication-year-2004\">2004<\/h2><ul class=\"publications-list\"><li>Motiejunas D (2004). <span class=\"publication-title\">Protein-protein docking assisted by sequence conservation and experimental data (Master&#8217;s Thesis)<\/span>, Molecular Biology, Ruperto-Carola University,Heidelberg <span style=\"color:#ddd; font-size:12px\">864<\/span><\/li><li>R.Hallingbaeck H (2004). <span class=\"publication-title\">Peroxidases: A computational study of ligand binding and enzyme kinetics (Master&#8217;s Thesis)<\/span>, Molecular Biotechnology, Uppsala University School of Engineering, Uppsala <span style=\"color:#ddd; font-size:12px\">865<\/span><\/li><\/ul><h2 id=\"publication-year-2003\">2003<\/h2><ul class=\"publications-list\"><li>Doudieu OMN (2003). <span class=\"publication-title\">Using Sequence Information in Protein Docking Procedures (Master&#8217;s Thesis)<\/span>, Bioinformatics, University of Applied Sciences, Berlin <span style=\"color:#ddd; font-size:12px\">866<\/span><\/li><li>Battey JN (2003). <span class=\"publication-title\">High-throughput Structural and Electrostatic Modelling of Ubiquitin Conjugating Enzymes (Master&#8217;s Thesis)<\/span>, Bioinformatics, Exeter University, Exeter <span style=\"color:#ddd; font-size:12px\">867<\/span><\/li><li>Pulagam LVP (2003). <span class=\"publication-title\">Structure-based design of inhibitors of enzymes of the ubiquitin mediated protein degradation pathway (Master&#8217;s Thesis)<\/span>, Bioinformatics, Cologne University Bioinformatics Center, University of Cologne <span style=\"color:#ddd; font-size:12px\">868<\/span><\/li><li>Neumann GF (2003). <span class=\"publication-title\">Entwicklung einer erweiterten Anwendung der Hauptkomponentenanalyse fuer das Protein-Protein Dockingproblem (Diploma Thesis)<\/span>, Physics, Ruperto-Carola University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1015<\/span><\/li><\/ul><h2 id=\"publication-year-2001\">2001<\/h2><ul class=\"publications-list\"><li>Ferrari S (2001). <span class=\"publication-title\">Inhibition studies of enzymes involved in drug resistance phenomena. Library-design and Structure-based approaches towards species-specific inhibitors of Thymidylate Synthase (PhD Thesis)<\/span>, University of Modena and Reggio Emilia, Modena <span style=\"color:#ddd; font-size:12px\">869<\/span><\/li><li>Gonzalez A (2001). <span class=\"publication-title\">Glycolytic Pathway Reaction Animations (Diploma Thesis)<\/span>, Biology, Ruperto-Carola University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1016<\/span><\/li><\/ul><h2 id=\"publication-year-1999\">1999<\/h2><ul class=\"publications-list\"><li>Nardi F (1999). <span class=\"publication-title\">Molecular Dynamics and NMR Spectroscopic Studies of Local Interactions of Small Peptides in Aqueous Solution Involving Aromatic Residues (PhD Thesis)<\/span>, Universite Joseph Fourier, Grenoble <span style=\"color:#ddd; font-size:12px\">870<\/span><\/li><li>Rienzo FD (1999). <span class=\"publication-title\">Computational studies of blue copper proteins (PhD Thesis)<\/span>, University of Modena and Reggio Emilia, Modena <span style=\"color:#ddd; font-size:12px\">871<\/span><\/li><li>Koboyashi M (1999). <span class=\"publication-title\">Chloride ion exchange routes in Haloalkane Dehalogenase from Xanthobacter autrophicus detected by Thermal Motion Pathway analysis, GRID and Essential Dynamics (Master&#8217;s Thesis)<\/span>, University of York <span style=\"color:#ddd; font-size:12px\">872<\/span><\/li><li>Gauges R (1999). <span class=\"publication-title\">Molekulardynamische Simulation zur Aufklaerung des Substratzuganges in Cytochrom P450eryF (Diploma Thesis)<\/span>, Biology, Eberhard-Karls University, Tubingen <span style=\"color:#ddd; font-size:12px\">1017<\/span><\/li><\/ul><h2 id=\"publication-year-1998\">1998<\/h2><ul class=\"publications-list\"><li>Bitomsky W (1998). <span class=\"publication-title\">Binding of Glycosaminoglycans to Heparin-Binding Proteins (PhD Thesis)<\/span>, University of Vienna <span style=\"color:#ddd; font-size:12px\">873<\/span><\/li><\/ul><h2 id=\"publication-year-1996\">1996<\/h2><ul class=\"publications-list\"><li>Ortiz AR (1996). <span class=\"publication-title\">Rational design of Human Synovial Fluid Phospholipase A2 inhibitors and analysis of their three-dimensional structure-activity relationships (PhD Thesis)<\/span>, University of Alcala de Henares, Madrid <span style=\"color:#ddd; font-size:12px\">874<\/span><\/li><li>Helms V (1996). <span class=\"publication-title\">Hydratation des aktiven Zentrums von Cytochrom P450cam &#8211; Untersuchung mit Molekueldynamik-Simulationen (PhD Thesis)<\/span>, Ludwig-Maximilians University, Munich <span style=\"color:#ddd; font-size:12px\">875<\/span><\/li><li>Reimer N (1996). <span class=\"publication-title\">Dynamische Einstellung des Parallelitaetsgrades mit reflexiven Programmen (Diploma Thesis)<\/span>, Computer Science, University of Karlsruhe, Tubingen <span style=\"color:#ddd; font-size:12px\">1018<\/span><\/li><\/ul><h2 id=\"publication-year-1995\">1995<\/h2><ul class=\"publications-list\"><li>Degenhardt M (1995). <span class=\"publication-title\">De-Novo Design von Liganden zur Blockierung der Substratzugaenlichkeit von Cytochrom P450cam (Diploma Thesis)<\/span>, Biology, Ruperto-Carola University, Heidelberg <span style=\"color:#ddd; font-size:12px\">1019<\/span><\/li><\/ul><h2 id=\"publication-year-1988\">1988<\/h2><ul class=\"publications-list\"><li>Wade R (1988). <span class=\"publication-title\">Ligand-Macromolecule Interactions (PhD Thesis)<\/span>, University of Oxford <span style=\"color:#ddd; font-size:12px\">850<\/span><\/li><\/ul>            <\/div>\n                                <div class=\"hits-tabs--tab\">\n              <\/ul><h2 id=\"publication-year-2013\">2013<\/h2><ul class=\"publications-list\"><li>Costi MP, Luciani R, Nerini E, D. G, Ferrari S, Venturelli A, Lazzari S, Wade RC, Henrich S, Motiejunas D (2013). <span class=\"publication-title\">Uso di inhibitori della Pteridina Reduttasi per la prevenzione e\/o il trattamento di infezioni parassitarie<\/span>, Italian Patent Nr. 1403584, Date of Patent: 31.10.2013, Filed : 25.11.2010 <span style=\"color:#ddd; font-size:12px\">1034<\/span><\/li><\/ul><h2 id=\"publication-year-2009\">2009<\/h2><ul class=\"publications-list\"><li>Costi MP, Marverti G, Cardinale D, Venturelli A, Ferrari S, Ponterini G, Henrich S, Salo-Ahen O, Wade RC (2009). <span class=\"publication-title\">Peptides binding to the dimer interface of thymidylate synthase for the treatment of cancer<\/span>,  United States Patent No.: US 8,916,679 B2, Date of Patent: 23.12.2014. Filed: 17.08.2012, 01.12.2009 <span style=\"color:#ddd; font-size:12px\">1033<\/span><\/li><\/ul>            <\/div>\n                  <\/div>\n      <\/div>\n\n  <\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":3,"featured_media":40653,"parent":42,"menu_order":5,"comment_status":"closed","ping_status":"closed","template":"page-templates\/group.php","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"hits-research-group":[1298],"class_list":["post-1344","page","type-page","status-publish","has-post-thumbnail","hentry","hits-research-group-mcm-de"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.2 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Publikationen - HITS gGmbH<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.h-its.org\/de\/forschung\/mcm\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"de_DE\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publikationen - 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