MCM Gruppe

Publikationen

2025

Reinhardt M, Bruce NJ, Kokh DB, Wade RC (2025). Correction to “Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics”, J. Chem. Theory Comput.,acs.jctc.5c01046 2071
Teuffel J, Mukherjee G, Han SB, Elstner M, Wade RC (2025). On the determinants of electron transfer reorganization energy in a cytochrome P450: cytochrome b5 complex. A combined quantum mechanics and molecular dynamics simulation study, The Journal of Chemical Physics 162(19),195101 2064
Athanasiou C, Cabezudo AC, Tsengenes A, Wade RC (2025). Simulation of Neurotrophin Receptor Transmembrane Helix Interactions Reveals Active States and Distinct Signaling Mechanisms, JACS Au,jacsau.5c00174 2063
Ferraz MV, Adan WCS, Lima TE, Santos AJ, Paula SOd, Dhalia R, Wallau GL, Wade RC, Viana IF, Lins RD (2025). Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning, PLoS Comput Biol 21(4):e1012921 2062
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’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). The need to implement FAIR principles in biomolecular simulations., Nat Methods. 2025 Apr 2. doi: 10.1038/s41592-025-02635-0. 2049

2024

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). Impact of an irreversible β-galactosylceramidase inhibitor on the lipid profile of zebrafish embryos, Computational and Structural Biotechnology Journal 23:1397-1407 1839
D’Arrigo G, Kokh DB, Nunes-Alves A, Wade RC (2024). Computational screening of the effects of mutations on protein-protein off-rates and dissociation mechanisms by τRAMD, Commun Biol 7(1),1159 1880
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). Comprehensive characterization of the neurogenic and neuroprotective action of a novel TrkB agonist using mouse and human stem cell models of Alzheimer’s disease, Stem Cell Res Ther 15(1),200 1886
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, Völkers M, Wade RC, Most P (2024). S100A1ct: A Synthetic Peptide Derived From S100A1 Protein Improves Cardiac Performance and Survival in Preclinical Heart Failure Models, Circulation,CIRCULATIONAHA.123.066961 2016
Paiardi G, Ferraz M, Rusnati M, Wade RC (2024). The accomplices: Heparan sulfates and N-glycans foster SARS-CoV-2 spike:ACE2 receptor binding and virus priming, Proc. Natl. Acad. Sci. U.S.A. 121(43),e2404892121 1872
Han SB, Teuffel J, Mukherjee G, Wade RC (2024). Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane‐bound cytochrome P450 2B4, Protein Science 33(10),e5165 1870
Gryn’ova G, Bereau T, Müller C, Friederich P, Wade RC, Nunes-Alves A, Soares TA, Merz K (2024). EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning, J. Chem. Inf. Model. 64(15):5737-5738 1855
Wade RC (2024). Editorial: The Journal of Molecular Recognition: Changing of the guard, J of Molecular Recognition 37(3),e3081 1840
Weidner P, Saar D, Söhn M, Schroeder T, Yu Y, Zöllner 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). Myotubularin-related-protein-7 inhibits mutant (G12V) K-RAS by direct interaction, Cancer Letters 588:216783 1841
Paiardi G, Milanesi M, Ferraz M, Zimmermann L, Urbinati C, Oreste P, Caccuri F, Chlanda P, Rusnati M, Wade RC (2024). The role of heparin in spike SARS-CoV-2 infection: From a model for heparan sulfates to a starting structure for antivirals, Biophysical Journal 123(3):157a-158a 1842
Schimunek J, Seidl P, Elez K, Hempel T, Le T, Noé 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’Arrigo G, Gianquinto E, Goßen J, Hanke A, Joseph BP, Kokh DB, Kovachka S, Manelfi C, Mukherjee G, Muñiz-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, Rodríguez ML, White KM, Fearon D, Delft Fv, Walsh MA, Horvath D, Brooks CL, Falsafi B, Ford B, García-Sastre A, Lee SY, Naffakh N, Varnek A, Klambauer G, Hermans TM (2024). A community effort in SARS‐CoV‐2 drug discovery, Molecular Informatics 43(1),e202300262 1723

2023

Rahman MT, Koski MK, Panecka-Hofman J, Schmitz W, Kastaniotis AJ, Wade RC, Wierenga RK, Hiltunen JK, Autio KJ (2023). An engineered variant of MECR reductase reveals indispensability of long-chain acyl-ACPs for mitochondrial respiration, Nat Commun 14(1),619 1583
Mukesh S, Mukherjee G, Singh R, Steenbuck N, Demidova C, Joshi P, Sangamwar AT, Wade RC (2023). Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance, Commun Chem 6(1),201 1719
Glaser M, Ritterhof J, Most P, Wade RC (2023). Wird KI neue Medikamente gegen Herzkrankheiten hervorbringen?, Aktuelle Kardiologie 12(06):450-458 1736
Roussaki M, Magoulas GE, Fotopoulou T, Santarem N, Barrias E, Pöhner I, Luelmo S, Afroudakis P, Georgikopoulou K, Nevado PT, Eick J, Bifeld E, Corral MJ, Jiménez-Antón 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). Design, synthesis and biological evaluation of antiparasitic dinitroaniline-ether phospholipid hybrids, Bioorganic Chemistry 138:106615 1677
Viviani LG, Kokh DB, Wade RC, Amaral AT (2023). Molecular Dynamics Simulations of the Human Ecto-5′-Nucleotidase (h-ecto-5′-NT, CD73): Insights into Protein Flexibility and Binding Site Dynamics, J. Chem. Inf. Model. 63(15):4691-4707 1690
Gomez GM, D’Arrigo G, Sanchez CP, Berger F, Wade RC, Lanzer M (2023). PfCRT mutations conferring piperaquine resistance in falciparum malaria shape the kinetics of quinoline drug binding and transport, PLoS Pathog 19(6):e1011436 1683
Muñiz‐Chicharro A, Votapka LW, Amaro RE, Wade RC (2023). Brownian dynamics simulations of biomolecular diffusional association processes, WIREs Comput Mol Sci 13(3),e1649 1555
Cabezudo AC, Athanasiou C, Tsengenes A, Wade RC (2023). Scaling Protein–Water Interactions in the Martini 3 Coarse-Grained Force Field to Simulate Transmembrane Helix Dimers in Different Lipid Environments, J. Chem. Theory Comput. 19(7):2109-2119 1635
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, Vivès RA, Nikitovic D, Blum SR (2023). Glycosaminoglycans: What Remains To Be Deciphered?, JACS Au 3(3):628-656 1636
Ferraz MVF, Neto JCS, Lins RD, Teixeira ES (2023). An artificial neural network model to predict structure-based protein–protein free energy of binding from Rosetta-calculated properties, Phys. Chem. Chem. Phys. 25(10):7257-7267 1784
Keulen SCv, Martin J, Colizzi F, Frezza E, Trpevski D, Diaz NC, Vidossich P, Rothlisberger U, Kotaleski JH, Wade RC, Carloni P (2023). Multiscale molecular simulations to investigate adenylyl cyclase‐based signaling in the brain, WIREs Comput Mol Sci 13(1),e1623 1493

2022

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’Arca D, Ponterini G, Costi MP (2022). Destabilizers of the thymidylate synthase homodimer accelerate its proteasomal degradation and inhibit cancer growth., Elife. 2022 Dec 7;11:e73862. doi: 10.7554/eLife.73862. 1557
Schmidt H, Mauer K, Glaser M, Dezfuli BS, Hellmann SL, Gomes ALS, Butter F, Wade RC, Hankeln T, Herlyn H (2022). Identification of antiparasitic drug targets using a multi-omics workflow in the acanthocephalan model, BMC Genomics 23(1),677 1513
Mendes MFdA, Bragatte MdS, Vianna P, Freitas MVd, Pöhner I, Richter S, Wade RC, Salzano FM, Vieira GF (2022). MatchTope: A tool to predict the cross reactivity of peptides complexed with Major Histocompatibility Complex I, Front. Immunol. 13,930590 1547
Dey D, Nunes-Alves A, Wade RC, Schreiber G (2022). Diffusion of small molecule drugs is affected by surface interactions and crowder proteins, iScience 25(10):105088 1599
Panecka-Hofman J, Poehner I, Wade RC (2022). Anti-trypanosomatid structure-based drug design – lessons learned from targeting the folate pathway, Expert Opinion on Drug Discovery 17(9):1029-1045 1514
Toral-Lopez A, Kokh DB, Marin EG, Wade RC, Godoy A (2022). Graphene BioFET sensors for SARS-CoV-2 detection: a multiscale simulation approach, Nanoscale Adv. 4(14):3065-3072 1511
Pöhner 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). Multitarget, Selective Compound Design Yields Potent Inhibitors of a Kinetoplastid Pteridine Reductase 1, J. Med. Chem. 65(13):9011-9033 1494
Eriksson O, Bhalla US, Blackwell KT, Crook SM, Keller D, Kramer A, Linne M, Saudargienė A, Wade RC, Kotaleski JH (2022). Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows, eLife 11,e69013 1495
Rusnati M, Paiardi G, Tobia C, Urbinati C, Lodola A, D’Ursi P, Corrado M, Castelli R, Wade RC, Tognolini M, Chiodelli P (2022). Cholenic acid derivative UniPR1331 impairs tumor angiogenesis via blockade of VEGF/VEGFR2 in addition to Eph/ephrin, Cancer Gene Ther 29(7):908-917 1283
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). Development and Biological Characterization of a Novel Selective TrkA Agonist with Neuroprotective Properties against Amyloid Toxicity, Biomedicines 10(3):614 1470
Eisenberg P, Albert L, Teuffel J, Zitzow E, Michaelis C, Jarick J, Sehlke C, Große L, Bader N, Nunes-Alves A, Kreikemeyer B, Schindelin H, Wade RC, Fiedler T (2022). The Non-phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase GapN Is a Potential New Drug Target in Streptococcus pyogenes, Front. Microbiol. 13,802427 1448
Paiardi G, Richter S, Oreste P, Urbinati C, Rusnati M, Wade RC (2022). The binding of heparin to spike glycoprotein inhibits SARS-CoV-2 infection by three mechanisms, Journal of Biological Chemistry 298(2):101507 1437

2021

Sadiq SK, Chicharro AM, Friedrich P, Wade RC (2021). Multiscale Approach for Computing Gated Ligand Binding from Molecular Dynamics and Brownian Dynamics Simulations, J. Chem. Theory Comput. 17(12):7912-7929 1305
Mukherjee G, Nandekar PP, Wade RC (2021). An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase, Commun Biol 4(1),55 1165
Aslam M, Kandasamy N, Ullah A, Paramasivam N, Öztürk 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). Putative second hit rare genetic variants in families with seemingly GBA-associated Parkinson’s disease, npj Genom. Med. 6(1),2 1208
Bianciotto M, Gkeka P, Kokh DB, Wade RC, Minoux H (2021). Contact Map Fingerprints of Protein–Ligand Unbinding Trajectories Reveal Mechanisms Determining Residence Times Computed from Scaled Molecular Dynamics, J. Chem. Theory Comput. 17(10):6522-6535 1280
Kokh DB, Wade RC (2021). G Protein-Coupled Receptor–Ligand Dissociation Rates and Mechanisms from τRAMD Simulations, J. Chem. Theory Comput. 17(10):6610-6623 1281
De M, Öztürk MA, Isbaner S, Tóth K, Wade RC (2021). DNA sequence-dependent positioning of the linker histone in a nucleosome: A single-pair FRET study, Biophysical Journal 120(17):3747-3763 1276
Nunes-Alves A, Ormersbach F, Wade RC (2021). Prediction of the Drug–Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis, J. Chem. Inf. Model. 61(7):3708-3721 1275
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 Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics, ACS Pharmacol. Transl. Sci. 4(3):1079-1095 1253
Reinhardt M, Bruce NJ, Kokh DB, Wade RC (2021). Brownian Dynamics Simulations of Proteins in the Presence of Surfaces: Long-Range Electrostatics and Mean-Field Hydrodynamics, J. Chem. Theory Comput. 17(6):3510-3524 1274
Glaser M, Bruce NJ, Han SB, Wade RC (2021). Simulation of the Positive Inotropic Peptide S100A1ct in Aqueous Environment by Gaussian Accelerated Molecular Dynamics, J. Phys. Chem. B 125(18):4654-4666 1267
Berger B, Amaral M, Kokh DB, Nunes-Alves A, Musil D, Heinrich T, Schröder M, Neil R, Wang J, Navratilova I, Bomke J, Elkins JM, Müller S, Frech M, Wade RC, Knapp S (2021). Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2, Cell Chemical Biology 28(5):686-698.e7 1215
Paiardi G, Milanesi M, Wade RC, D’Ursi P, Rusnati M (2021). A Bittersweet Computational Journey among Glycosaminoglycans, Biomolecules 11(5):739 1273
Dey D, Marciano S, Nunes-Alves A, Kiss V, Wade RC, Schreiber G (2021). Line-FRAP, A Versatile Method to Measure Diffusion Rates In Vitro and In Vivo, Journal of Molecular Biology 433(9):166898 1224
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). Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development, Processes 9(1):71 1162
Moreau CA, Quadt KA, Piirainen H, Kumar H, Bhargav SP, Strauss L, Tolia NH, Wade RC, Spatz JP, Kursula I, Frischknecht F (2021). A function of profilin in force generation during malaria parasite motility that is independent of actin binding, J Cell Sci 134(5):jcs233775 1214
Ganotra GK, Nunes-Alves A, Wade RC (2021). A Protocol to Use Comparative Binding Energy Analysis to Estimate Drug-Target Residence Time, In „Protein-Ligand Interactions and Drug Design“, Methods in Molecular Biology (MIMB), 2266:171-186 1252
Nunes-Alves A, Kokh DB, Wade RC (2021). Ligand unbinding mechanisms and kinetics for T4 lysozyme mutants from τRAMD simulations, Current Research in Structural Biology 3:106-111 1268

2020

Nunes-Alves A, Mazzolari A, Merz KM (2020). What Makes a Paper Be Highly Cited? 60 Years of the Journal of Chemical Information and Modeling, J. Chem. Inf. Model. 60(12):5866-5867 1161
Mustafa G, Nandekar PP, Mukherjee G, Bruce NJ, Wade RC (2020). The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics, Sci Rep 10(1),7284 1132
Öztürk MA, Wade RC (2020). Computation of FRAP recovery times for linker histone – chromatin binding on the basis of Brownian dynamics simulations, Biochimica et Biophysica Acta (BBA) – General Subjects 1864(10):129653 1135
Nunes-Alves A, Kokh DB, Wade RC (2020). Recent progress in molecular simulation methods for drug binding kinetics, Current Opinion in Structural Biology 64:126-133 1138
Kokh DB, Doser B, Richter S, Ormersbach F, Cheng X, Wade RC (2020). A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories, J. Chem. Phys. 153(12):125102 1142
Mazzolari A, Nunes-Alves A, Wahab HA, Amaro RE, Cournia Z, Merz KM (2020). Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry, J. Chem. Inf. Model. 60(7):3328-3330 1137
Weidner P, Söhn M, Schroeder T, Helm L, Hauber V, Gutting T, Betge J, Röcken C, Rohrbacher FN, Pattabiraman VR, Bode JW, Seger R, Saar D, Nunes-Alves A, Wade RC, Ebert MPA, Burgermeister E (2020). Myotubularin-related protein 7 activates peroxisome proliferator-activated receptor-gamma, Oncogenesis 9(6),59 1143
Sadiq SK (2020). Fine-Tuning of Sequence Specificity by Near Attack Conformations in Enzyme-Catalyzed Peptide Hydrolysis, Catalysts 10(6):684 1209
Diestelkoetter‐Bachert P, Beck R, Reckmann I, Hellwig A, Garcia‐Saez A, Zelman‐Hopf M, Hanke A, Alves AN, Wade RC, Mayer MP, Wieland F (2020). Structural characterization of an Arf dimer interface: molecular mechanism of Arf‐dependent membrane scission, FEBS Lett,1873-3468.13808 1134
Öztürk MA, De M, Cojocaru V, Wade RC (2020). Chromatosome Structure and Dynamics from Molecular Simulations, Annu. Rev. Phys. Chem. 71(1):101-119 1007
Yuan J, Han SB, Richter S, Wade RC, Kokh DB (2020). Druggability Assessment in TRAPP Using Machine Learning Approaches, J. Chem. Inf. Model. 60(3):1685-1699 1091
Holderbach S, Adam L, Jayaram B, Wade RC, Mukherjee G (2020). RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features, Frontiers in Molecular Biosciences 7:393 1159
Berger B, Amaral M, Kokh DB, Nunes-Alves A, Musil D, Heinrich T, Schröder M, Neil R, Wang J, Navratilova I, Bomke J, Elkins JM, Müller S, Frech M, Wade RC, Knapp S (2020). Structure-Kinetic-Relationship Reveals the Mechanism of Selectivity of FAK Inhibitors Over PYK2, SSRN Journal 1168

2019

Bruce NJ, Narzi D, Trpevski D, Keulen SCv, Nair AG, Röthlisberger U, Wade RC, Carloni P, Kotaleski JH (2019). Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals, PLoS Comput Biol 15(10):e1007382 544
Nunes-Alves A (2019). From Brazil to Germany: Challenges and Advantages, J. Chem. Inf. Model. 60(2):449-451 742
Mustafa G, Nandekar PP, Bruce NJ, Wade RC (2019). Differing Membrane Interactions of Two Highly Similar Drug-Metabolizing Cytochrome P450 Isoforms: CYP 2C9 and CYP 2C19, IJMS 20(18):4328 935
Calogeropoulou T, Magoulas GE, Pöhner I, Panecka-Hofman J, Linciano P, Ferrari S, Santarem N, Jiménez-Antón MD, Olías-Molero AI, Alunda JM, Silva ACd, Wade RC, Costi MP (2019). Hits and Lead Discovery in the Identification of New Drugs against the Trypanosomatidic Infections, Medicinal Chemistry of Neglected and Tropical Diseases: Advances in the Design and Synthesis of Antimicrobial Agents, Eds Venkatesan Jayaprakash, Daniele Castagnolo, Yusuf Özkay, Chapter 10, pp 185-231, CRC Press 727
Bruce NJ, Ganotra GK, Richter S, Wade RC (2019). KBbox: A Toolbox of Computational Methods for Studying the Kinetics of Molecular Binding, J. Chem. Inf. Model. 59(9):3630-3634 543
Kokh DB, Kaufmann T, Kister B, Wade RC (2019). Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times, Front. Mol. Biosci. 6,36 548
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). Allostery in Its Many Disguises: From Theory to Applications, Structure 27(4):566-578 549
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, Pöhner I, Müller 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). Accelerating Drug Discovery Efforts for Trypanosomatidic Infections Using an Integrated Transnational Academic Drug Discovery Platform, SLAS DISCOVERY: Advancing the Science of Drug Discovery 24(3):346-361 1075
Mustafa G, Nandekar PP, Camp TJ, Bruce NJ, Gregory MC, Sligar SG, Wade RC (2019). Influence of Transmembrane Helix Mutations on Cytochrome P450-Membrane Interactions and Function, Biophysical Journal 116(3):419-432 551
Lyonnais S, Sadiq SK, Lorca-Oró 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, Tisné C, Gorelick RJ, Mirambeau G (2019). The HIV-1 ribonucleoprotein dynamically regulates its condensate behavior and drives acceleration of protease activity through membrane-less granular phase-separation, biorxiv;528638v2,[Preprint] 1009
Schmidt TT, Sharma S, Reyes GX, Gries K, Gross M, Zhao B, Yuan J, Wade R, Chabes A, Hombauer H (2019). A genetic screen pinpoints ribonucleotide reductase residues that sustain dNTP homeostasis and specifies a highly mutagenic type of dNTP imbalance, Nucleic Acids Research 47(1):237-252 728
Wade RC, Salo-Ahen O (2019). Molecular Modeling in Drug Design, Molecules 24(2):321 552
Mukherjee G, Nandekar P, Mustafa G, Richter S, Wade RC (2019). A Multi-resolution Approach to the Simulation of Protein Complexes in a Membrane Bilayer, High Performance Computing in Science and Engineering ‚ 18,pp.505-514,Springer International Publishing 934

2018

Ganotra GK, Wade RC (2018). Prediction of Drug–Target Binding Kinetics by Comparative Binding Energy Analysis, ACS Med. Chem. Lett. 9(11):1134-1139 385
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, Müller W, Wittig U, Luciani R, Sesenna A, Quotadamo A, Ferrari S, Pöhner I, Cordeiro-da-Silva A, Mangani S, Costantino L, Costi MP (2018). Enhancement of Benzothiazoles as Pteridine Reductase-1 Inhibitors for the Treatment of Trypanosomatidic Infections, J. Med. Chem. 62(8):3989-4012 1008
Begolo D, Vincent IM, Giordani F, Pöhner I, Witty MJ, Rowan TG, Bengaly Z, Gillingwater K, Freund Y, Wade RC, Barrett MP, Clayton C (2018). The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing, PLoS Pathog 14(9):e1007315 380
Sadiq SK, Mirambeau G, Meyerhans A (2018). Equilibrium model of drug-modulated GagPol-embedded HIV-1 reverse transcriptase dimerization to enhance premature protease activation, AIDS Research and Human Retroviruses 34(9):804-807 389
Öztürk MA, Cojocaru V, Wade RC (2018). Toward an Ensemble View of Chromatosome Structure: A Paradigm Shift from One to Many, Structure 26(8):1050-1057 384
Douglas RG, Nandekar P, Aktories J, Kumar H, Weber R, Sattler JM, Singer M, Lepper S, Sadiq SK, Wade RC, Frischknecht F (2018). Inter-subunit interactions drive divergent dynamics in mammalian and textitPlasmodium actin filaments, PLoS Biol 16(7):e2005345 390
Foerster JM, Poehner I, Ullmann GM (2018). MCMap – A Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions, ACS Omega 3(6):6465-6475 381
Heroven C, Georgi V, Ganotra GK, Brennan P, Wolfreys F, Wade RC, Fernández-Montalván AE, Chaikuad A, Knapp S (2018). Halogen–Aromatic pi Interactions Modulate Inhibitor Residence Times, Angew. Chem. Int. Ed. 57(24):7220-7224 387
Heroven C, Georgi V, Ganotra GK, Brennan P, Wolfreys F, Wade RC, Fernández-Montalván AE, Chaikuad A, Knapp S (2018). Halogenaromatische pi-Wechselwirkungen modulieren die Verweilzeit von Inhibitoren, Angew. Chem. 130(24):7338-7343 388
Sultan CS, Saackel A, Stank A, Fleming T, Fedorova M, Hoffmann R, Wade RC, Hecker M, Wagner AH (2018). Impact of carbonylation on glutathione peroxidase-1 activity in human hyperglycemic endothelial cells, Redox Biology 16:113-122 392
Kokh DB, Amaral M, Bomke J, Grädler U, Musil D, Buchstaller H, Dreyer MK, Frech M, Lowinski M, Vallee F, Bianciotto M, Rak A, Wade RC (2018). Estimation of Drug-Target Residence Times by τ-Random Acceleration Molecular Dynamics Simulations, J. Chem. Theory Comput. 14(7):3859-3869 382
Öztürk MA, Cojocaru V, Wade RC (2018). Dependence of Chromatosome Structure on Linker Histone Sequence and Posttranslational Modification, Biophysical Journal 114(10):2363-2375 383
Bruce NJ, Ganotra GK, Kokh DB, Sadiq SK, Wade RC (2018). New approaches for computing ligand–receptor binding kinetics, Current Opinion in Structural Biology 49:1-10 386
Sadiq SK, Wade RC (2018). Computing Protein-Ligand Binding Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics Simulations, Biophysical Journal 114 (3), 56a 729

2017

Amaral M, Kokh DB, Bomke J, Wegener A, Buchstaller HP, Eggenweiler HM, Matias P, Sirrenberg C, Wade RC, Frech M (2017). Protein conformational flexibility modulates kinetics and thermodynamics of drug binding, Nat Commun 8(1),2276 266
Farnham A, Kurz C, Öztürk 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). Early career researchers want Open Science, Genome Biol 18(1),221 268
Panecka-Hofman J, Pöhner I, Spyrakis F, Zeppelin T, Pisa FD, Iacono LD, Bonucci A, Quotadamo A, Venturelli A, Mangani S, Costi M, Wade RC (2017). Comparative mapping of on-targets and off-targets for the discovery of anti-trypanosomatid folate pathway inhibitors, Biochimica et Biophysica Acta (BBA) – General Subjects 1861(12):3215-3230 274
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 novel homozygous ARL13B variant in patients with Joubert syndrome impairs its guanine nucleotide-exchange factor activity, Eur J Hum Genet 25(12):1324-1334 275
Linciano P, Dawson A, Pöhner I, Costa DM, Sá 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, Alcântara LM, Bertolacini CP, Fontana V, Wittig U, Müller W, Wade RC, Hunter WN, Mangani S, Costantino L, Costi MP (2017). Exploiting the 2-Amino-1,3,4-thiadiazole Scaffold To Inhibit Trypanosoma brucei Pteridine Reductase in Support of Early-Stage Drug Discovery, ACS Omega 2(9):5666-5683 270
Jedwabny W, Panecka-Hofman J, Dyguda-Kazimierowicz E, Wade RC, Sokalski WA (2017). Application of a simple quantum chemical approach to ligand fragment scoring for Trypanosoma brucei pteridine reductase 1 inhibition, J Comput Aided Mol Des 31(8):715-728 269
Stank A, Kokh DB, Horn M, Sizikova E, Neil R, Panecka J, Richter S, Wade RC (2017). TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets., Nucleic Acids Research 45(W1):W325-W330 277
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, Müller-Fahrnow A, Ecker GF (2017). Kinetics for Drug Discovery: an industry-driven effort to target drug residence time, Drug Discovery Today 22(6):896-911 276
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 unique profilin-actin interface is important for malaria parasite motility, PLoS Pathog 13(5):e1006412 271
Nillegoda NB, Stank A, Malinverni D, Alberts N, Szlachcic A, Barducci A, Rios PDL, Wade RC, Bukau B (2017). Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes., eLife 6,e24560 272
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, Pöhner I, Wade R, Costi M, Mangani S (2017). Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity, Molecules 22(3):426 267
Öztürk MA, Cojocaru V, Wade RC (2017). Drosophila melanogaster linker histone (dH1) binding to the nucleosome., 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 273

2016

Tong R, Wade RC, Bruce NJ (2016). Comparative electrostatic analysis of adenylyl cyclase for isoform dependent regulation properties, Proteins 84(12):1844-1858 171
Sadiq SK (2016). Reaction–diffusion basis of retroviral infectivity, Phil. Trans. R. Soc. A 374:20160148 169
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, Jiménez-García B, Moal IH, Férnandez-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). Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment, Proteins 84:323-348 180
Ozboyaci M, Martinez M, Wade RC (2016). An efficient low storage and memory treatment of gridded interaction fields for simulations of macromolecular association, J. Chem. Theory Comput. 12(9):4563-4577 173
Öztürk MA, Pachov GV, Wade RC, Cojocaru V (2016). Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome, Nucleic Acids Res 44(14):6599-6613 176
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, Jiménez-Antón MD, Corral MJ, Alunda JM, Pellati F, Wade RC, Ferrari S, Mangani S, Costi MP (2016). Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs, J. Med. Chem. 59(16):7598-7616 174
Schibich D, Gloge F, Pöhner I, Björkholm P, Wade RC, Heijne Gv, Bukau B, Kramer G (2016). Global profiling of SRP interaction with nascent polypeptides, Nature 536(7615):219-223 172
Stank A, Richter S, Wade RC (2016). ProSAT+: visualizing sequence annotations on 3D structure, Protein Engineering, Design and Selection 29(8):281-284 178
Wild K, Bange G, Motiejunas D, Kribelbauer J, Hendricks A, Segnitz B, Wade RC, Sinning I (2016). Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex, Journal of Molecular Biology 428(14):2880-2897 177
Subramanian SR, Singam ERA, Berinski M, Subramanian V, Wade RC (2016). Identification of an Electrostatic Ruler Motif for Sequence-Specific Binding of Collagenase to Collagen, J. Phys. Chem. B 120(33):8580-8589 179
Pöhner IA, Panecka J, Wade RC (2016). What determines docking performance in drug discovery? A case study of PTR1, an anti-parasitic target, Journal of Cheminformatics 2016, 8(Suppl 1):P46 553
Stank A, Kokh DB, Fuller JC, Wade RC (2016). Protein Binding Pocket Dynamics, Acc. Chem. Res. 49(5):809-815 181
Gdynia G, Sauer SW, Kopitz J, Fuchs D, Duglova K, Ruppert T, Miller M, Pahl J, Cerwenka A, Enders M, Mairbäurl H, Kamiński 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). The HMGB1 protein induces a metabolic type of tumour cell death by blocking aerobic respiration, Nat Commun 7(1),10764 735
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). The immunomodulation potential of the synthetic derivatives of benzothiazoles: Implications in immune system disorders through in vitro and in silico studies, Bioorganic Chemistry 64:21-28 187
Rafiullah R, Aslamkhan M, Paramasivam N, Thiel C, Mustafa G, Wiemann S, Schlesner M, Wade RC, Rappold GA, Berkel S (2016). Homozygous missense mutation in the LMAN2L gene segregates with intellectual disability in a large consanguineous Pakistani family, J Med Genet 53(2):138-144 185
Gundić M, Tomić A, Wade RC, Matovina M, Karačić Z, Kazazić S, Tomić S (2016). Human DPP III – Keap1 Interactions: A Combined Experimental And Computational study, Croat. Chem. Acta 2016, 89(2), 217–228 170
Kokh DB, Czodrowski P, Rippmann F, Wade RC (2016). Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets, J. Chem. Theory Comput. 12(8):4100-4113 175
Ozboyaci M, Kokh DB, Wade RC (2016). Three steps to Gold: Mechanism of protein adsorption to a gold surface revealed by Brownian and molecular dynamics simulations, Phys. Chem. Chem. Phys. 18(15):10191-10200 182
Yu X, Kokh DB, Nandekar P, Mustafa G, Richter S, Wade RC (2016). Dynathor: Dynamics of the Complex of Cytochrome P450 and Cytochrome P450 Reductase in a Phospholipid Bilayer, High Performance Computing in Science and Engineering ´15,pp.255-264,Springer International Publishing 184
Ozboyaci M, Kokh DB, Corni S, Wade RC (2016). Modeling and simulation of protein–surface interactions: achievements and challenges, Quart. Rev. Biophys. 49,e4 186
Yu X, Nandekar P, Mustafa G, Cojocaru V, Lepesheva GI, Wade RC (2016). Ligand tunnels in T. brucei and human CYP51: Insights for parasite-specific drug design, Biochimica et Biophysica Acta (BBA) – General Subjects 1860(1):67-78 188

2015

Mustafa G, Nandekar PP, Yu X, Wade RC (2015). On the application of the MARTINI coarse-grained model to immersion of a protein in a phospholipid bilayer, The Journal of Chemical Physics 143(24):243139 555
Garg D, Skouloubris S, Briffotaux J, Myllykallio H, Wade RC (2015). Conservation and Role of Electrostatics in Thymidylate Synthase, Sci Rep 5(1),17356 556
Romanowska J, Kokh DB, Wade RC (2015). When the Label Matters: Adsorption of Labeled and Unlabeled Proteins on Charged Surfaces, Nano Lett. 15(11):7508-7513 557
Liu L, Wade RC, Heermann DW (2015). A multiscale approach to simulating the conformational properties of unbound multi-C2H2 zinc finger proteins, Proteins 83(9):1604-1615 560
Martinez M, Bruce NJ, Romanowska J, Kokh DB, Ozboyaci M, Yu X, Öztürk MA, Richter S, Wade RC (2015). SDA 7: A modular and parallel implementation of the simulation of diffusional association software, J. Comput. Chem. 36(21):1631-1645 561
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). Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation, Nature 524(7564):247-251 559
Dinh TV, Bienvenut WV, Linster E, Feldman-Salit A, Jung VA, Meinnel T, Hell R, Giglione C, Wirtz M (2015). Molecular identification and functional characterization of the first Nα-acetyltransferase in plastids by global acetylome profiling, Proteomics 15(14):2426-2435 562
Yu X, Martinez M, Gable AL, Fuller JC, Bruce NJ, Richter S, Wade RC (2015). webSDA: a web server to simulate macromolecular diffusional association, Nucleic Acids Res 43(W1):W220-W224 564
Seybold C, Elserafy M, Rüthnick D, Ozboyaci M, Neuner A, Flottmann B, Heilemann M, Wade RC, Schiebel E (2015). Kar1 binding to Sfi1 C-terminal regions anchors the SPB bridge to the nuclear envelope, The Journal of Cell Biology 209(6):843-861 563
Romanowska J, Kokh DB, Fuller JC, Wade RC (2015). Computational Approaches for Studying Drug Binding Kinetics, Thermodynamics and Kinetics of Drug Binding,pp.211-235,Wiley-VCH Verlag GmbH & Co. KGaA 567
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). Hotspots in an Obligate Homodimeric Anticancer Target. Structural and Functional Effects of Interfacial Mutations in Human Thymidylate Synthase, J. Med. Chem. 58(8):3572-3581 565
Fuller JC, Martinez M, Henrich S, Stank A, Richter S, Wade RC (2015). LigDig: a web server for querying ligand–protein interactions, Bioinformatics 31(7):1147-1149 569
Bruce NJ, Kokh DB, Ozboyaci M, Wade RC (2015). Modelling of solvation effects for brownian dynamics simulation of biomolecular recognition., IAS series 28:259-280 566
Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BFF, Pawlik A, Blomberg N (2015). A Quick Guide for Building a Successful Bioinformatics Community., PLoS Comput Biol 11(2):e1003972 738
Yu X, Cojocaru V, Mustafa G, Salo-Ahen OMH, Lepesheva GI, Wade RC (2015). Dynamics of CYP51: implications for function and inhibitor design, J. Mol. Recognit. 28(2):59-73 568
Budd A, Dinkel H, Corpas M, Fuller JC, Rubinat L, Devos DP, Khoueiry PH, Förstner KU, Georgatos F, Rowland F, Sharan M, Binder JX, Grace T, Traphagen K, Gristwood A, Wood NT (2015). Ten Simple Rules for Organizing an Unconference, PLoS Comput Biol 11(1):e1003905 737
Rosa M, Kokh DB, Corni S, Wadet R, Felice RD (2015). Docking of DNA duplexes on a gold surface, JSAME 2015(1):1-18 554
Tomić A, Berynskyy M, Wade RC, Tomić S (2015). Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding, Mol. BioSyst. 11(11):3068-3080 558

2014

Fuller JC, Martinez M, Wade RC (2014). On Calculation of the Electrostatic Potential of a Phosphatidylinositol Phosphate-Containing Phosphatidylcholine Lipid Membrane Accounting for Membrane Dynamics, PLoS ONE 9(8):e104778 571
Mustafa G, Yu X, Wade RC (2014). Drug Metabolism Prediction, Wiley 572
Mereghetti P, Martinez M, Wade RC (2014). Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules, BMC Biophys 7(1):4 570

2013

Gombos L, Neuner A, Berynskyy M, Fava LL, Wade RC, Sachse C, Schiebel E (2013). GTP regulates the microtubule nucleation activity of γ-tubulin, Nat Cell Biol 15(11):1317-1327 573
Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC (2013). Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria, PLoS Comput Biol 9(7):e1003159 575
Feldman-Salit A, Hering S, Messiha HL, Veith N, Cojocaru V, Sieg A, Westerhoff HV, Kreikemeyer B, Wade RC, Fiedler T (2013). Regulation of the Activity of Lactate Dehydrogenases from Four Lactic Acid Bacteria, J. Biol. Chem. 288(29):21295-21306 576
Mereghetti P, Wade RC (2013). Brownian dynamics simulation of protein diffusion in crowded environments, AIP Conference Proceedings,pp.511-516,American Institute of Physics 579
Sandikci A, Gloge F, Martinez M, Mayer MP, Wade R, Bukau B, Kramer G (2013). Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding, Nat Struct Mol Biol 20(7):843-850 574
Kokh DB, Richter S, Henrich S, Czodrowski P, Rippmann F, Wade RC (2013). TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins, J. Chem. Inf. Model. 53(5):1235-1252 577
Balbo J, Mereghetti P, Herten D, Wade R (2013). The Shape of Protein Crowders is a Major Determinant of Protein Diffusion, Biophysical Journal 104(7):1576-1584 578
Garg D, Beribisky AV, Ponterini G, Ligabue A, Marverti G, Martello A, Costi MP, Sattler M, Wade RC (2013). Translational repression of thymidylate synthase by targeting its mRNA, Nucleic Acids Research 41(7):4159-4170 581
Fuller JC, Khoueiry P, Dinkel H, Forslund K, Stamatakis A, Barry J, Budd A, Soldatos TG, Linssen K, Rajput AM (2013). Biggest challenges in bioinformatics, EMBO Rep 14(4):302-304 739
Ferrari S, Ingrami M, Soragni F, Wade RC, Costi MP (2013). Ligand-based discovery of N-(1,3-dioxo-1H,3H-benzo[de]isochromen-5-yl)-carboxamide and sulfonamide derivatives as thymidylate synthase A inhibitors, Bioorganic & Medicinal Chemistry Letters 23(3):663-668 583
Yu X, Cojocaru V, Wade RC (2013). Conformational diversity and ligand tunnels of mammalian cytochrome P450s, Biotechnology and Applied Biochemistry 60(1):134-145 580
Berynskyy M, Wade RC (2013). Treating Conformational Flexibility in Protein-Protein Docking, CPC 3(1):27-35 582

2012

Oguchi Y, Kummer E, Seyffer F, Berynskyy M, Anstett B, Zahn R, Wade RC, Mogk A, Bukau B (2012). A tightly regulated molecular toggle controls AAA+ disaggregase, Nat Struct Mol Biol 19(12):1338-1346 584
Brancolini G, Kokh DB, Calzolai L, Wade RC, Corni S (2012). Docking of Ubiquitin to Gold Nanoparticles, ACS Nano 6(11):9863-9878 585
Biedermannová L, Prokop Z, Gora A, Chovancová E, Kovács M, Damborský J, Wade RC (2012). A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB, J. Biol. Chem. 287(34):29062-29074 587
Stein M, Pilli M, Bernauer S, Habermann BH, Zerial M, Wade RC (2012). The Interaction Properties of the Human Rab GTPase Family – A Comparative Analysis Reveals Determinants of Molecular Binding Selectivity, PLoS ONE 7(4):e34870 588
Mereghetti P, Wade RC (2012). Atomic Detail Brownian Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions, J. Phys. Chem. B 116(29):8523-8533 586
Feldman-Salit A, Wirtz M, Lenherr E, Throm C, Hothorn M, Scheffzek K, Hell R, Wade R (2012). Allosterically Gated Enzyme Dynamics in the Cysteine Synthase Complex Regulate Cysteine Biosynthesis in Arabidopsis thaliana, Structure 20(2):292-302 589
Cojocaru V, Winn PJ, Wade RC (2012). Multiple, Ligand-dependent Routes from the Active Site of Cytochrome P450 2C9, CDM 13(2):143-154 590

2011

Mereghetti P, Wade RC (2011). Diffusion of hydrophobin proteins in solution and interactions with a graphite surface, BMC Biophys 4(1),9 594
Wade RC (2011). Das biomolekulare Erkennungspuzzle, Spektrum der Wissenschaft – Extra, 14 – 17 740
Salo-Ahen OMH, Wade RC (2011). The active-inactive transition of human thymidylate synthase: Targeted molecular dynamics simulations, Proteins 79(10):2886-2899 593
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). Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase, Proceedings of the National Academy of Sciences 108(34):E542-E549 591
Cojocaru V, Balali-Mood K, Sansom MSP, Wade RC (2011). Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9, PLoS Comput Biol 7(8):e1002152 592
Pachov GV, Gabdoulline RR, Wade RC (2011). On the structure and dynamics of the complex of the nucleosome and the linker histone, Nucleic Acids Research 39(12):5255-5263 598
Sundar RS, Gopalakrishnan R, Wade RC, Subramanian V (2011). Structural Basis for the Varying Propensities of Different Amino Acids To Adopt the Collagen Conformation, J. Phys. Chem. B 115(11):2593-2607 595
Kokh DB, Wade RC, Wenzel W (2011). Receptor flexibility in small-molecule docking calculations, WIREs Comput Mol Sci 1(2):298-314 596
Cohavi O, Reichmann D, Abramovich R, Tesler AB, Bellapadrona G, Kokh DB, Wade RC, Vaskevich A, Rubinstein I, Schreiber G (2011). A Quantitative, Real-Time Assessment of Binding of Peptides and Proteins to Gold Surfaces, Chem. Eur. J. 17(4):1327-1336 600
Ferrari S, Morandi F, Motiejunas D, Nerini E, Henrich S, Luciani R, Venturelli A, Lazzari S, Calò S, Gupta S, Hannaert V, Michels PAM, Wade RC, Costi MP (2011). Virtual Screening Identification of Nonfolate Compounds, Including a CNS Drug, as Antiparasitic Agents Inhibiting Pteridine Reductase, J. Med. Chem. 54(1):211-221 599
Mereghetti P, Kokh D, McCammon JA, Wade RC (2011). Diffusion and association processes in biological systems: theory, computation and experiment, BMC Biophys 4(1):2 597

2010

Mereghetti P, Gabdoulline RR, Wade RC (2010). Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties, Biophysical Journal 99(11):3782-3791 605
Kaur-Ghumaan S, Schwartz L, Lomoth R, Stein M, Ott S (2010). Katalytische Wasserstofferzeugung an einem einkernigen Eisen(II)-Carbonylkomplex als kleinstes funktionelles Modell für das aktive Zentrum von [FeFe]-Hydrogenasen, Angewandte Chemie 122(43):8207-8211 601
Kaur-Ghumaan S, Schwartz L, Lomoth R, Stein M, Ott S (2010). Catalytic Hydrogen Evolution from Mononuclear Iron(II) Carbonyl Complexes as Minimal Functional Models of the [FeFe] Hydrogenase Active Site, Angewandte Chemie International Edition 49(43):8033-8036 602
Wirtz M, Birke H, Heeg C, Müller C, Hosp F, Throm C, König S, Feldman-Salit A, Rippe K, Petersen G, Wade RC, Rybin V, Scheffzek K, Hell R (2010). Structure and Function of the Hetero-oligomeric Cysteine Synthase Complex in Plants, J. Biol. Chem. 285(43):32810-32817 604
Garg D, Henrich S, Salo-Ahen OMH, Myllykallio H, Costi MP, Wade RC (2010). Novel Approaches for Targeting Thymidylate Synthase To Overcome the Resistance and Toxicity of Anticancer Drugs, J. Med. Chem. 53(18):6539-6549 606
Klipp E, Wade RC, Kummer U (2010). Biochemical network-based drug-target prediction, Current Opinion in Biotechnology 21(4):511-516 607
Pachov GV, Gabdoulline RR, Wade RC (2010). Kinetics of Biomacromolecular Complex Formation: Theory and Experiment, Protein-Protein Complexes,pp.89-118,IMPERIAL COLLEGE PRESS 614
Löscher S, Gebler A, Stein M, Sanganas O, Buhrke T, Zebger I, Dau H, Friedrich B, Lenz O, Haumann M (2010). Protein-Protein Complex Formation Affects the Ni-Fe and Fe-S Centers in the H2-Sensing Regulatory Hydrogenase from Ralstonia eutropha H16, Chem. Eur. J. of Chem. Phys. 11(6):1297-1306 603
Kokh DB, Corni S, Winn PJ, Hoefling M, Gottschalk KE, Wade RC (2010). ProMetCS: An Atomistic Force Field for Modeling Protein−Metal Surface Interactions in a Continuum Aqueous Solvent, J. Chem. Theory Comput. 6(5):1753-1768 608
O’Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ (2010). Visualization of macromolecular structures, Nat Methods 7(S3):S42-S55 609
Cardinale D, Salo-Ahen O, Guaitoli G, Ferrari S, Venturelli A, Franchini S, Battini R, Ponterini G, Wade R, Costi M (2010). Design and characterization of a mutation outside the active site of human thymidylate synthase that affects ligand binding, Protein Engineering, Design and Selection 23(2):81-89 611
Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC (2010). Comparative binding energy analysis for binding affinity and target selectivity prediction, Proteins 78(1):135-153 615
Kaur-Ghumaan S, Schwartz L, Lomoth R, Stein M, Ott S (2010). Katalytische Wasserstofferzeugung an einem einkernigen Eisen(II)- Carbonylkomplex als kleinstes funktionelles Modell fuer das aktive Zentrum von [FeFe]-Hydrogenasen, Angewandte Chemie 122(43):8207-8211 666
Löscher S, Gebler A, Stein M, Sanganas O, Buhrke T, Zebger I, Dau H, Friedrich B, Lenz O, Haumann M (2010). Protein-protein complex formation affects the Ni-Fe and Fe-S centers in the H2-sensing regulatory hydrogenase from Ralstonia eutropha H16., Chem. Eur. J. of Chem. Phys. 11(6):1297-1306 667
Kokh DB, Corni S, Winn PJ, Hoefling M, Gottschalk KE, Wade RC (2010). ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Aqueous Solvent, J. Chem. Theory Comput. 6(5):1753-1768 669
Michielin O, Wade RC (2010). Foreword Preface to the JMR Special Issue on ‘Dynamic Aspects of Molecular Recognition’, J. Mol. Recognit., 23: 101-101 670
Cardinale D, Salo-Ahen O, Guaitoli G, Ferrari S, Venturelli A, Franchini S, Battini R, Ponterini G, Wade R, Costi M (2010). Homodimeric Enzymes as Drug Targets, Protein Engineering, Design and Selection 23(2):81-89 671

2009

Singh PS, Rudbeck HC, Huang P, Ezzaher S, Eriksson L, Stein M, Ott S, Lomoth R (2009). (I,0) Mixed-Valence State of a Diiron Complex with Pertinence to the [FeFe]-Hydrogenase Active Site: An IR, EPR, and Computational Study, Inorg. Chem. 48(23):10883-10885 618
Pavlova M, Klvana M, Prokop Z, Chaloupkova R, Banas P, Otyepka M, Wade RC, Tsuda M, Nagata Y, Damborsky J (2009). Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate, Nat Chem Biol 5(10):727-733 619
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). Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations, Journal of Molecular Biology 392(5):1339-1356 620
Huang B (2009). MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction, OMICS: A Journal of Integrative Biology 13(4):325-330 616
Pachov GV, Gabdoulline RR, Wade RC (2009). Computational Simulations of Protein– Protein and Protein– Nucleic Acid Association, CRC Press 622
Gabdoulline RR, Wade RC (2009). On the Contributions of Diffusion and Thermal Activation to Electron Transfer between Phormidium laminosum Plastocyanin and Cytochrome f: Brownian Dynamics Simulations with Explicit Modeling of Nonpolar Desolvation Interactions and Electron Transfer Events, J. Am. Chem. Soc. 131(26):9230-9238 621
Müller C, Frau MAG, Ballinari D, Colombo S, Bitto A, Martegani E, Airoldi C, van Neuren AS, Stein M, Weiser J, Battistini C, Peri F (2009). Design, Synthesis, and Biological Evaluation of Levoglucosenone-Derived Ras Activation Inhibitors, ChemMedChem 4(4):524-528 617
Pachov GV, Wade RC (2009). Docking of a Linker Histone to The Nucleosome With Flexible Linker DNAs, Biophysical Journal 96(3):83a-84a 623
Kokh DB, Huang B, Wade RC, Winn PJ (2009). Modeling of Protein Adsorption on a Metal Surface: Brownian Dynamics Simulations, Biophysical Journal 96(3):298a-299a 624
Feldman-Salit A, Wirtz M, Hell R, Wade RC (2009). A Mechanistic Model of the Cysteine Synthase Complex, Journal of Molecular Biology 386(1):37-59 625
Stein M, Gabdoulline RR, Wade RC (2009). Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields, Mol. BioSyst. 6(1):162-174 612
Gabdoulline RR, Wade RC (2009). On the contributions of diffusion and thermal activation to electron transfer between Phormidium laminosum plastocyanin and cytochrome f: Brownian dynamics simulations with explicit modeling of nonpolar desolvation interactions and electron transfer events., J. Am. Chem. Soc. 131(26):9230-9238 677
Pachov GV, Gabdoulline RR, Wade RC (2009). Computational Simulations of Protein-Protein and Protein-Nucleic Acid Association., In “ Computational Protein-Protein Interactions“, Eds. R. Nussinov and G. Schreiber, Taylor and Francis Group LLC, Boca Raton:109–128 678
Cohavi O, Corni S, Rienzo FD, Felice RD, Gottschalk KE, Hoefling M, Kokh D, Molinari E, Schreiber G, Vaskevich A, Wade RC (2009). Protein–surface interactions: challenging experiments and computations, J. Mol. Recognit., 23: 259-262 1130
Henrich S, Salo-Ahen OMH, Huang B, Rippmann FF, Cruciani G, Wade RC (2009). Computational approaches to identifying and characterizing protein binding sites for ligand design, J. Mol. Recognit., 23: 209-219 1131

2008

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). SYCAMORE–a systems biology computational analysis and modeling research environment, Bioinformatics 24(12):1463-1464 630
Motiejunas D, Gabdoulline R, Wang T, Feldman-Salit A, Johann T, Winn PJ, Wade RC (2008). Protein-protein docking by simulating the process of association subject to biochemical constraints, Proteins 71(4):1955-1969 632
Richter S, Wenzel A, Stein M, Gabdoulline RR, Wade RC (2008). webPIPSA: a web server for the comparison of protein interaction properties, Nucleic Acids Research 36(Web Server):W276-W280 629
Witan H, Kern A, Koziollek-Drechsler I, Wade R, Behl C, Clement AM (2008). Heterodimer formation of wild-type and amyotrophic lateral sclerosis-causing mutant Cu/Zn-superoxide dismutase induces toxicity independent of protein aggregation, Human Molecular Genetics 17(10):1373-1385 631
Hegermann J, Halbedel S, Dumke R, Regula J, Gabdoulline RR, Mayer F, Stülke J, Herrmann R (2008). The acidic, glutamine-rich Mpn474 protein of Mycoplasma pneumoniae is surface exposed and covers the complete cell, Microbiology 154(4):1185-1192 628
Henrich S, Richter S, Wade R (2008). On the use of PIPSA to Guide Target-Selective Drug Design, ChemMedChem 3(3):413-417 635
Bauer R, Woelkart K, Salo-Ahen O (2008). CB Receptor Ligands from Plants, CTMC 8(3):173-186 626
Salo-Ahen O (2008). Editorial: The Medicinal Chemistry of Agents Targeting the Endogenous Cannabinoid System, CTMC 8(3):172-172 627
Stein M, Gabdoulline R, Wade R (2008). Calculating enzyme kinetic parameters from protein structures, Biochemical Society Transactions 36(1):51-54 633
Bertoša B, Kojić-Prodić B, Wade RC, Tomić S (2008). Mechanism of Auxin Interaction with Auxin Binding Protein (ABP1): A Molecular Dynamics Simulation Study, Biophysical Journal 94(1):27-37 634
Bertoša B, Kojić-Prodić B, Wade RC, Tomić S (2008). Mechanism of auxin interaction with auxin binding protein (ABP1): a molecular dynamics simulation study, Biophysical Journal 94(1):27-37 683

2007

Feldman-Salit A, Wade RC (2007). Molecular Recognition: Computational Analysis and Modelling, In Wiley Encyclopedia of Chemical Biology, T.P. Begley (Ed.), 1-10, John Wiley & Sons, Inc. 1129
Wade RC (2007). Exploring biomolecular recognition by modelling and simulation, Modelling and Simulation in Science,pp.150-153,WORLD SCIENTIFIC 640
Löscher S, Schwartz L, Stein M, Ott S, Haumann M (2007). Facilitated Hydride Binding in an Fe−Fe Hydrogenase Active−Site Biomimic Revealed by X-ray Absorption Spectroscopy and DFT Calculations, Inorg. Chem. 46(26):11094-11105 637
Eilers G, Schwartz L, Stein M, Zampella G, de Gioia L, Ott S, Lomoth R (2007). Ligand versus Metal Protonation of an Iron Hydrogenase Active Site Mimic, Chem. Eur. J. 13(25):7075-7084 636
Pachov G, Gabdoulline RR, Wade RC (2007). Simulation of linker histone-chromatin interactions, 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 36:69-74 641
.Winn PJ, Zahran M, Wade RC (2007). Comparisons of the protein electrostatic potentials as a means to understanding function, Proceedings of the International School of Physics “Enrico Fermi”, (2007) pages 207-219 645
Stein M, Gabdoulline RR, Besson B, Wade RC (2007). The estimation of kinetic parameters in systems biology by comparing molecular interaction fields of enzymes., Beilstein Proceedings of the 2nd Conference on Experimental Standard Conditions of Enzyme Characterizations,Ruedesheim, 19-23 March, 2006, (2007) pages 237-253 647
Cruciani G, Carosati E, Wade RC, Baroni M (2007). Characterization of protein-binding sites and ligands using molecular interaction fields., Comprehensive Medicinal Chemistry II, (2007) volume 4, pages 237-253 650
Wang T, Wade RC (2007). On the Use of Elevated Temperature in Simulations To Study Protein Unfolding Mechanisms, J. Chem. Theory Comput. 3(4):1476-1483 642
Winn PJ, Zahran M, Battey JN, Zhou Y, Wade RC, Banerjee A (2007). Structural and electrostatic properties of ubiquitination and related pathways., Front Biosci 12(8-12):3419 643
Tomić S, Bertoša B, Wang T, Wade RC (2007). COMBINE analysis of the specificity of binding of Ras proteins to their effectors, Proteins 67(2):435-447 644
Stein M, Gabdoulline RR, Wade RC (2007). Bridging from molecular simulation to biochemical networks, Current Opinion in Structural Biology 17(2):166-172 639
Karyakin A, Motiejunas D, Wade RC, Jung C (2007). FTIR studies of the redox partner interaction in cytochrome P450: The Pdx–P450cam couple, Biochimica et Biophysica Acta (BBA) – General Subjects 1770(3):420-431 646
Cojocaru V, Winn PJ, Wade RC (2007). The ins and outs of cytochrome P450s, Biochimica et Biophysica Acta (BBA) – General Subjects 1770(3):390-401 648
Gabdoulline RR, Stein M, Wade RC (2007). qPIPSA: Relating enzymatic kinetic parameters and interaction fields, BMC Bioinformatics 8(1):373 638
Winn PJ, Zahran M, Battey JN, Zhou Y, Wade RC, Banerjee A (2007). Structural and electrostatic properties of ubiquitination and related pathways, Front Biosci 12(8-12):3419 685
Winn P, Zahran M, Wade R (2007). Proceedings of the International School of Physics „Enrico Fermi“ workshop on Protein Folding and Drug Design, In Comparisons of Protein Electrostatic Potentials as a Means to Understanding Function 733
Karyakin A, Motiejunas D, Wade R, Jung C (2007). FTIR studies of the redox partner interaction in cytochrome P450: The Pdx-P450cam couple, Biochimica et Biophysica Acta. General Subjects 1770:420–431 745
Motiejunas D, Wade R (2007). Structural, Energetic, and Dynamic Aspects of Ligand–Receptor Interactions, Comprehensive Medicinal Chemistry II,pp.193-213,Elsevier 1128

2006

Stein M, Gabdoulline R, Beßon B, Wade R (2006). Beilstein Proceedings of the 2nd Conference on ’Experimental Standard Conditions of Enzyme Characterizations (ESCEC)’ em Ruedesheim (2007) em, In The Estimation of Kinetic Parameters in Systems Biology by Comparing Molecular Interaction Fields of Enzymes, pp. 237–253, 19-23 March 746
Stein M, Gabdoulline RR, Wade RC (2006). Integrating Structural and Kinetic Enzymatic Information in Systems Biology, In NIC Workshop 2006 ’From Computational Biophysics to Systems Biology’, 6–9 June, John von Neumann Institute for Computing, Juelich, vol. 34 of NIC Series, pp. 129–132 689
K. S, T. W, R.C. W (2006). Molecular Docking, In Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, pp. pp1149–1153, Ed. Ganten,D. and Ruckpaul, K., Springer 690
Gabdoulline RR, Ulbrich S, Richter S, Wade RC (2006). ProSAT2-Protein Structure Annotation Server, Nucleic Acids Research 34(Web Server):W79-W83 691
Hallingbäck HR, Gabdoulline RR, Wade RC (2006). Comparison of the binding and reactivity of plant and mammalian peroxidases to indole derivatives by computational docking, Biochemistry 45(9):2940-2950 692
Spaar A, Dammer C, Gabdoulline RR, Wade RC, Helms V (2006). Diffusional encounter of barnase and barstar, Biophysical Journal 90(6):1913-1924 693
Wang T, Wade RC (2006). Force Field Effects on a beta-sheet Protein Domain Structure in Thermal Unfolding Simulations, J. Chem. Theory Comput. 2(1):140-148 694
Jalkanen KJ, Jürgensen 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). Use of Vibrational Spectroscopy to Study Protein and DNA Structure, Hydration, and Binding of Biomolecules: A Combined Theoretical and Experimental Approach, Int. J. Quantum Chem. 106(5):1160-1198 695
Cruciani G, Carosati E, Wade R, Baroni M (2006). Characterization of Protein- Binding Sites and Ligands Using Molecular Interaction Fields, In Comprehensive Medicinal Chemistry II, vol. 4, pp. 237–253, Ed. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford 747
Motiejunas D, Wade R (2006). Structural, Energetic and Dynamic Aspects of Ligand-Receptor Interactions, In Comprehensive Medicinal Chemistry II, vol. 4, pp. pp.193–213, Ed. Triggle, D.J. and Taylor, J.B., Elsevier: Oxford 748
Stein M, Gabdoulline R, Wade R (2006). From Computational Biophysics to Systems Biology 2006, In Integrating Structural and Kinetic Enzymatic Information in Systems Biology, vol. 34 of NIC Series, pp. 129–132, Hansmann, Ulrich H.E.; Meinke, Jan; Mohanty, Sandipan; Zimmermann, Olav (Eds.) 749
Wang T, Wade R (2006). Force Field Effects on a b-sheet Protein Domain Structure in Thermal Unfolding Simulations, J Chem Theory and Comput 2:140–148 750

2005

Wade RC, Motiejunas D, Schleinkofer K, Sudarko PJW, Banerjee A, Kariakin A, Jung C (2005). Multiple molecular recognition mechanisms. Cytochrome P450–A case study, Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics 1754(1-2):239-244 696
Wade RC (2005). Calculation and Application of Molecular Interaction Fields, In Molecular Interaction Fields. Applications in Drug Discovery and ADME Prediction, pp. Ch. 2, pp27–42, Ed. Cruciani, G., Wiley-VCH, Weinheim, ISBN 3-527-31087-8 697
McCammon JA, Wade RC (2005). Pushing the limits: Editorial overview, Current Opinion in Structural Biology 15(2):135-136 698
Schleinkofer K, Sudarko PJW, Lüdemann SK, Wade RC (2005). Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?, EMBO Rep 6(6):584-589 699
Wade RC (2005). Recognition Highlights and Commentaries, Current Opinion in Structural Biology 15(2):135-136 700
Kmunícek J, Hynková K, Jedlicka T, Nagata Y, Negri A, Gago F, Wade RC, Damborský J (2005). Quantitative Analysis of Substrate Specificity of Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26, Biochemistry 44(9):3390-3401 701
Winn PJ, Battey JN, Schleinkofer K, Banerjee A, Wade RC (2005). Issues in High-Throughput Comparative Modelling: A Case Study Using the Ubiquitin E2 Conjugating Enzymes, Current Opinion in Structural Biology 15(2):135-136 702
Ehrlich LP, Nilges M, Wade RC (2005). The Impact of Protein Flexibility on Protein-protein Docking, Proteins 58(1):126-133 703
McCammon J, Wade R (2005). Pushing the limits: Editorial Overview. Curr, Opin. Struct. Biol. 15:135–136 751
Ulbrich S (2005). The Protein Structure Annotation Tool ProSAT2, Studienarbeit 1026

2004

Wade RC, Henrich S, Wang T (2004). Using 3D protein structures to derive 3D-QSARs, Drug Discovery Today: Technologies 1(3):241-246 704
Schleinkofer K, Wiedemann U, Otte L, Wang T, Krause G, Oschkinat H, Wade RC (2004). Comparative Structural and Energetic Analysis of WW Domain-Peptide Interactions, Journal of Molecular Biology 344(3):865-881 705
Winn PJ, Religa TL, Battey JN, Banerjee A, Wade RC (2004). Determinants of Functionality in the Ubiquitin Conjugating Enzyme Family, Structure 12(9):1563-1574 706
Wang T, Tomic S, Gabdoulline RR, Wade RC (2004). How Optimal are the Binding Energetics of Barnase and Barstar?, Biophysical Journal 87(3):1618-1630 707
Rienzo FD, Gabdoulline RR, Wade RC, Sola M, Menziani MC (2004). Computational approaches to structural and functional analysis of plastocyanin and other blue copper proteins, Cellular and Molecular Life Sciences (CMLS) 61(10):1123-1142 708
Wade RC, Winn PJ, Schlichting I, Sudarko (2004). A survey of active site access channels in cytochromes P450, Journal of Inorganic Biochemistry 98(7):1175-1182 709
Damborsky J, Kmunicek J, Jedlicka T, Luengo S, Gago F, Ortiz AR, Wade RC (2004). Rational Re-design of Haloalkane Dehalogenases Guided by Comparative Binding Energy Analysis, In Enzyme functionality: Design, Engineering and Screening, pp. pp79–96, Ed. A. Svendsen, Marcel Dekker, New York 710

2003

Zemojtel T, Wade RC, Dandekar T (2003). In Search of the Prototype of Nitric Oxide Synthase, FEBS Letters 554(1-2):1-5 711
Ferrari S, Costi PM, Wade RC (2003). Inhibitor specificity via protein dynamics: Insights from design of antibacterial agents targeted against thymidylate synthase, Chemistry & Biology 10(12):1183-1193 712
Bertoša B, Kojić-Prodić B, Wade RC, Ramek M, Piperaki S, Tsantili-Kakoulidou A, Tomić S (2003). 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, J. Chem. Inf. Comput. Sci. 43(5):1532-1541 713
Essigke T, Ullmann GM, Wade RC (2003). What Determines the Redox Potential of Ferredoxins?, In „Proceedings of the 13th International Conference on Cytochromes P450“, pp. 25–30, Monduzzi Editore, Bologna 714
Kmuníček J, Boháč M, Luengo S, Gago F, Wade RC, Damborský J (2003). Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations, J. Comput. Aided Mol. Des. 17:299–311 715
Gabdoulline R, Wade RC, Walther D (2003). MolSurfer: a macromolecular interface navigator, Nucleic Acids Research 31(13):3349-3351 716
Gabdoulline RR, Kummer U, Olsen LF, Wade RC (2003). Concerted Simulations Reveal How Peroxidase Compound III Formation Results in Cellular Oscillations, Biophysical Journal 85(3):1421-1428 717
Gabdoulline RR, Hoffmann R, Leitner F, Wade RC (2003). ProSAT: Functional annotation of protein 3D structures, Bioinformatics 19(13):1723-1725 718
Finocchiaro G, Wang T, Hoffmann R, Gonzalez A, C. R (2003). DSMM – a Database of Simulated Molecular Motions, Nucleic Acids Research 31(1):456-457 719
Wang T, Wade RC (2003). Implicit Solvent Models for Flexible Protein-protein Docking by Molecular Dynamics Simulation, Proteins 50(1):158-169 720
Essigke T, Ullmann M, Wade R (2003). Proceedings of the 13textsuperscriptth International Conference on Cytochromes P450, In What Determines the Redox Potential of Ferredoxins?, pp. pp25–30, Monduzzi Editore, Bologna 752

2002

Deprez E, Gill E, Helms V, Wade RC, Hoa GHB (2002). Specific and Non-specific Effects of Potassium Cations on Substrate-protein Interactions in Cytocromes P450cam and P450lin, Journal of Inorganic Biochemistry 91(4):597-606 721
Wang T, Wade RC (2002). Comparative Binding Energy (COMBINE) Analysis of OppA−Peptide Complexes to Relate Structure to Binding Thermodynamics, J. Med. Chem. 45(22):4828-4837 722
Winn PJ, Ludemann SK, Gauges R, Lounnas V, Wade RC (2002). 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, Proceedings of the National Academy of Sciences 99(8):5361-5366 723
Gabdoulline RR, Wade RC (2002). Biomolecular diffusional association, Current Opinion in Structural Biology 12(2):204-213 724
Banerjee A, Wade RC (2002). Elusive recognition determinants for ubiquitination, J. Mol. Recognit. 15(1):3-5 725
Rienzo FD, Gabdoulline RR, Wade RC, Menziani MC (2002). Biologically relevant properties of copper-containing proteins analysed by means of semi-quantitative and quantitative theoretical descriptors, In Handbook of Copper Pharmacology and Toxicology, pp. pp. 53–80, Ed. E. J. Massaro, Humana Press, Totowa, New Jersey 726

2001

Rienzo FD, Gabdoulline RR, Menziani MC, Benedetti PGD, Wade RC (2001). Electrostatic Analysis and Brownian Dynamics Simulation of the Association of Plastocyanin and Cytochrome F, Biophysical Journal 81(6):3090-3104 753
Kmuníček J, Luengo S, Gago F, Ortiz AR, Wade RC, Damborský J (2001). Comparative Binding Energy (COMBINE) Analysis of the Substrate Specificity of Haloalkane Dehalogenase from Xanthobacter Autotrophicus GJ10, Biochemistry 40(30):8905-8917 754
Wang T, Wade RC (2001). Comparative Binding Energy (COMBINE) analysis of Influenza Neuraminidase-Inhibitor Complexes, J. Med. Chem. 44(6):961-971 755
Gabdoulline RR, Wade RC (2001). Protein-protein Association: Investigation of Factors Influencing Association Rates by Brownian Dynamics Simulations, Journal of Molecular Biology 306(5):1139-1155 756
Luedemann S, Gabdoulline R, Lounnas V, Wade R (2001). Substrate access to cytochrome P450cam investigated by molecular dynamics simulations: An interactive look at the underlying mechanisms, Internet. J. Chem., 4, 6 757
Wade RC, Gabdoulline RR, Rienzo FD (2001). Protein Interaction Property Similarity Analysis, Int. J. Quantum Chem. 83(3-4):122-127 758
Tomic S, Wade R (2001). COMBINE Analysis of Nuclear Receptor-DNA Binding Specificity: Comparison of Two Data Sets, Croat. Chem. Acta. 74:295–314 759
Ehrlich LP, Wade RC (2001). Protein-Protein Docking, Reviews in Computational Chemistry,pp.61-97,John Wiley & Sons, Inc. 760
Jalkanen K, Nieminen R, Frimand K, Bohr J, Bohr H, Wade R, Tajkhorshid E, Suhai S (2001). A Comparison of Aqueous Solvent Models Used in the Calculation of the Raman and ROA spectra of L-alanine, Chemical Physics 265(2):125-151 761
Wang T, Wade R (2001). COMBINE 3D-QSAR analysis of Influenza Neuraminidase Inhibitors, In Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships, pp. pp78–82, Eds. Holtje, H-D., Sippl,W., Prous Science S.A., Barcelona 762
Wade R (2001). Derivation of QSARs using 3D Structural Models of Protein-ligand complexes by COMBINE Analysis, In Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships, pp. pp23–28, Eds. Holtje, H-D., Sippl,W., Prous Science S.A., Barcelona 763

2000

Lamotte-Brasseur J, Dubus A, Wade RC (2000). pKa calculations for class C beta-lactamases: The role of tyr-150, Proteins 40:23–28 769
Lüdemann SK, Lounnas V, Wade RC (2000). 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, Journal of Molecular Biology 303(5):797-811 764
Lüdemann SK, Lounnas V, Wade RC (2000). How do substrates enter and products exit the buried active site of cytochrome P450cam? 2. Steered molecular dynamics and adiabatic mapping of substrate pathways, Journal of Molecular Biology 303(5):813-830 765
Das B, Helms V, Lounnas V, Wade RC (2000). Multicopy molecular dynamics simulations suggest how to reconcile crystallographic and product formation data for camphor enantiomers bound to cytochrome P-450cam, Journal of Inorganic Biochemistry 81(3):121-131 766
Rienzo FD, Gabdoulline R, Menziani MC, Wade R (2000). Blue Copper Proteins: A Comparative Analysis of their Molecular Interaction Properties, Protein Sci. 9(8):1439-1454 767
Nardi F, Kemmink J, Sattler M, Wade RC (2000). The cisProline(i-1)-Aromatic(i) Interaction: Folding of the Ala-cisPro-Tyr peptide characterized by NMR and theoretical approaches, J. Biomol. NMR 17:63–77 768
Tomic S, Nilsson L, Wade RC (2000). Nuclear receptor-DNA binding specificity: a COMBINE and Free-Wilson QSAR analysis, J. Med. Chem. 43(9):1780-1792 770
Tomić S, Nilsson L, Wade RC (2000). COMBINE and Free-Wilson QSAR analysis of nuclear receptor – DNA binding, Molecular Modeling and Prediction of Bioactivity,pp.269-270,Springer US 771

1999

Blomberg N, Gabdoulline RR, Nilges M, Wade RC (1999). Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity, Proteins 37(3):379-387 937
Gabdoulline RR, Wade RC (1999). On the protein-protein diffusional encounter complex, J. Mol. Recognit. 12(4):226-234 938
Gabdoulline R, Wade R, Walter D (1999). MolSurfer: 2D maps to navigate 3D structures of proteins and their complexes, Trends in Biochem. Sci. 24:285–287 772
Nielsen JE, Andersen KV, Honig B, Hooft RWW, Klebe G, Vriend G, Wade RC (1999). Improving macromolecular electrostatics calculations, Protein Engineering, Design and Selection 12(8):657-662 774
Elcock AH, Gabdoulline RR, Wade RC, McCammon J (1999). Computer Simulation of Protein-Protein Association Kinetics: Acetylcholinesterase-Fasciculin, Journal of Molecular Biology 291(1):149-162 775
Ibragimova GT, Wade RC (1999). Stability of the beta-sheet of the WW domain: A Molecular Dynamics Simulation Study, Biophysical Journal 77(4):2191-2198 777
Bitomsky W, Wade RC (1999). Docking of Glycosaminoglycans to Heparin-binding Proteins: Validation for aFGF, bFGF and Antithrombin and Application to IL-8, J. Am. Chem. Soc. 121(13):3004-3013 778
Lounnas V, Lüdemann SK, Wade RC (1999). Towards molecular dynamics simulations of large proteins with a hydration shell at constant presssure, Biophysical Chemistry 78(1-2):157-182 779
Lamotte-Brasseur J, Lounnas V, Raquet X, Wade RC (1999). pKa calculations for class A beta-lactamases: influence of substrate binding, Protein Science 8(2):404-409 780
Nardi F, Wade R (1999). Ways and Means to Enhance the Configurational Sampling of Small Peptides in Aqueous Solution in Molecular Dynamics Simulations, In Theoretical and Computational Chemistry Book Series, vol. 7, pp. Ch. 21, 859–898, Eds. Balbuena,P.B. and Seminario,J.M., Elsevier Science: Amsterdam, Netherlands 781
Knapp-Mohammady M, Jalkanen K, Nardi F, Wade R, Suhai S (1999). 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, Chemical Physics 240(1-2):63-77 782
Linge JP, Nilges M, Ehrlich L (1999). StarDOM: From STAR format to XML, Journal of Biomolecular NMR,15(2):169-172 942

1998

Helms V, Wade RC (1998). Hydration energy landscape of the active site cavity in cytochrome P450cam, Proteins 32(3):381-396 939
Wade RC, Gabdoulline RR, Luty BA (1998). Species dependence of enzyme-substrate encounter rates for triose phosphate isomerases, Proteins 31(4):406-416 940
Gabdoulline RR, Wade RC (1998). Brownian Dynamics Simulation of Protein–Protein Diffusional Encounter, Methods 14(3):329-341 795
Ringrose L, Lounnas V, Ehrlich L, Buchholz F, Wade R, Stewart A (1998). Comparative Kinetic Analysis of FLP and Cre Recombinases: Mathematical Models for DNA Binding and Recombination, Journal of Molecular Biology 284(2):363-384 783
Worth GA, Nardi F, Wade RC (1998). Use of Multiple Molecular Dynamics Trajectories to Study Biomolecules in Solution: The YTGP Peptide, J. Phys. Chem. B 102(32):6260-6272 784
Wade RC, Gabdoulline RR, Ludemann SK, Lounnas V (1998). Electrostatic steering and ionic tethering in enzyme-ligand binding: Insights from simulations, Proceedings of the National Academy of Sciences 95(11):5942-5949 785
Tomic S, Gabdoulline R, Kojic-Prodic B, Wade R (1998). Classification of auxin related compounds based on similarity of their interaction fields: Extension to a new set of compounds, Internet J. Chem. 1:26 786
Ibragimova GT, Wade RC (1998). Importance of explicit salt ions for protein stability in molecular dynamics simulation, Biophysical Journal 74(6):2906-2911 787
Helms V, Wade RC (1998). Computational Alchemy to Calculate Absolute Protein-Ligand Binding Free Energy, J. Am. Chem. Soc. 120(12):2710-2713 788
Madura JD, Briggs JM, Wade RC, Gabdoulline RR (1998). Brownian Dynamics, John Wiley & Sons, Ltd 792
Tomić S, Gabdoulline RR, Kojić-Prodić B, Wade RC (1998). Classification of auxin plant hormones by interaction property similarity indices, J. Comput. Aided Mol. Des. 12:63–79 793
Ehrlich L, Reczko M, Bohr H, Wade RC (1998). Prediction of protein hydration sites from sequence by modular neural networks, Protein Engineering Design and Selection 11(1):11-19 794
Wade RC, Lüdemann S (1998). Computational Strategies for Modeling Receptor Flexibility in Studies of Receptor-Ligand Interactions, Structure-Based Drug Design,pp.41-52,Springer Netherlands 796
Wade RC, Sobolev V, Ortiz AR, Peters G (1998). Computational Approaches to Modeling Receptor Flexibility Upon Ligand Binding: Application to Interfacially Activated Enzymes, Structure-Based Drug Design,pp.223-232,Springer Netherlands 797
Wade RC, Ortiz AR, Gago F (1998). Comparative binding energy analysis, Perspectives in Drug Discovery and Design, 9:19-34 943

1997

Helms V, Wade RC (1997). Free energies of hydration from thermodynamic integration: Comparison of molecular mechanics force fields and evaluation of calculation accuracy, J. Comput. Chem. 18(4):449-462 941
Wade RC (1997). ’Flu’ and Structure Based Drug Design, Structure 5(9):1139-1145 798
Raquet X, Lounnas V, Lamotte-Brasseur J, Frère J, Wade R (1997). pKa Calculations for Class A Beta-lactamases: Methodological and Mechanistic Implications, Biophysical Journal 73(5):2416-2426 799
Sobolev V, Moallem TM, Wade RC, Vriend G, Edelman M (1997). CASP2 molecular docking predictions with the LIGIN software, Proteins Suppl 1:210–214 800
Lüdemann SK, Carugo O, Wade RC (1997). Substrate Access to Cytochrome P450cam: a Comparison of a Thermal Motion Pathway Analysis with Molecular Dynamics Simulation Data, Journal of Molecular Modeling 3(8):369-374 801
Nardi F, Worth GA, Wade RC (1997). Local interactions of aromatic residues in short peptides in aqueous solution: a combined database and energetic analysis, Folding and Design 2:S62-S68 802
Lounnas V, Wade RC (1997). Exceptionally stable salt-bridges in cytochrome P450cam have functional roles, Biochemistry 36(18):5402-5417 803
Gabdoulline R, Wade R (1997). Simulation of the Diffusional Association of Barnase and Barstar, Biophysical Journal 72(5):1917-1929 804
Ortiz AR, Pastor M, Palomer A, Cruciani G, Gago F, Wade RC (1997). Reliability of CoMFA Models: Effects of Data Scaling and Variable Selection Using a Set of Human Synovial Fluid Phospholipase A2 Inhibitors, J. Med. Chem. 40(7):1136-1148 805
Helms V, Wade R (1997). Free energies of hydration from thermodynamic integration: A comparison of molecular mechanics force fields and evaluation of calculations accuracy, J. Comp. Chem. 18:449–462 806

1996

Sobolev V, Wade R, Vriend G, Edelman M (1996). Molecular Docking Using Surface Complementarity, Proteins 25:120-129 814
Gabdoulline R, Wade R (1996). Analytically defined surfaces to analyze molecular interaction properties, Journal of Molecular Graphics 14(6):341-353 807
Demchuk E, Wade RC (1996). Improving the Continuum Dielectric Approach to Calculating pKas of Ionizable Groups in Proteins, J. Phys. Chem. 100(43):17373-17387 808
Wade R, Oschkinat H (1996). Influence of glycosylation on the activity of rG-CSFs: in vitro studies: molecular structure and modeling, Intl. J. Hematology 64:Suppl. 2, S1-S2, S7-S8 809
Schulze H, Hoa GHB, Helms V, Wade RC, Jung C (1996). Structural Changes in cytochrome P-450cam effected by the binding of the enantiomers (1R)-Camphor and (1S)-Camphor, Biochemistry 35(45):14127-14138 810
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). Fundamentals of Enzyme-Ligand Interactions in Cytochrome P450cam, p. 3, Ed. M.J. Geisow, BIODIGM, Nottingham 811
Worth GA, Lecuyer C, Wade RC (1996). TRAJAN: A Tool to Analyze Trajectories from Molecular Simulations, Journal of Molecular Graphics 14(3):173-182 812
Peters G, Olsen O, Svendsen A, Wade R (1996). Theoretical investigation of the dynamics of the Active Site Lid in Rhizomucor Miehei Lipase, Biophysical Journal 71(1):119-129 813
Gabdoulline RR, Wade RC (1996). Effective charges for Macromolecules in Solvent, J. Phys. Chem. 100(9):3868-3878 815
Helms V, Deprez E, Gill E, Barret C, Hoa GHB, Wade RC (1996). Improved binding of cytochrome P450cam substrate analogues designed to fill extra space in the substrate binding pocket, Biochemistry 35(5):1485-1499 816
Wade RC (1996). Brownian dynamics simulations of enzyme-substrate encounter, Biochemical Society Transactions 24(1):254-259 817
Reimer N, Hänßgen SU, Tichy WF (1996). Dynamically adapting the degree of parallelism with reflexive programs, Parallel Algorithms for Irregularly Structured Problems 1117:313-318,Springer Berlin Heidelberg 851

1995

Ortiz A, Pisabarro M, Gago F, Wade R (1995). Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis: Application to Human Synovial Fluid Phospholipase A2 Inhibitors, In QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications, pp. pp439–443, Eds. Sanz,F., Giraldo,J., Manaut,F, J.R. Prous Science Publishers, Barcelona 818
Worth GA, Wade RC (1995). Aromatic – (i+2) Amine Interaction in Peptides, J. Phys. Chem. 99(48):17473-17482 819
Wade R (1995). Simulation of enzyme-substrate interactions: the diffusional encounter step, Acta Bioch. Polon. 42:419–425 820
Worth G, Wade R (1995). Molecular Dynamics Study of Short Peptide Sequences from BPTI displaying aromatic-amide interactions, In AIP Conference Proceedings 821
Degenhardt M, Wade R (1995). De novo design of ligands to block substrate access to cytochrome P450cam, J. Mol. Model. 1:93 822
Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, Ilin A, Antosiewicz J, Gilson MK, Bagheri B, Scott L, McCammon J (1995). Electrostatics and Diffusion of Molecules in Solution: Simulations with the University of Houston Brownian Dynamics Program, Computer Physics Communications 91(1-3):57-95 823
Helms V, Wade R (1995). Thermodynamics of Water Mediating Protein-Ligand Interactions in Cytochrome P450cam: A Molecular Dynamics Study, Biophysical Journal 69(3):810-824 824
Ortiz AR, Pisabarro MT, Gago F, Wade RC (1995). Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis, J. Med. Chem. 38(14):2681-2691 825

1994

Madura JD, Davist ME, Gilson MK, Wades RC, Luty BA, McCammon JA (1994). Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations, Reviews in Computational Chemistry,pp.229-267,John Wiley & Sons, Inc. 826
Pisabarro M, Palomer A, Ortiz A, Wade R, Gago F, Mauleón D, Carganico G (1994). Rational Drug Design: GRID- and LUDI-based Structural Modifications of a Human Synovial Fluid Phospholipase A2 Inhibitor Leading to Enhanced Activity., Journal of Molecular Graphics 12(1):72 827
Wade RC, Luty BA, Demchuk E, Madura JD, Davis ME, Briggs JM, McCammon JA (1994). Simulation of Enzyme-Substrate Encounter with Gated Active Sites, Nat Struct Mol Biol 1(1):65-69 828
Pisabarro MT, Ortiz AR, Palomer A, Cabre F, Garcia L, Wade RC, Gago F, Mauleon D, Carganico G (1994). Rational Modification of Human Synovial Fluid Phospholipase A2 Inhibitors, J. Med. Chem. 37(3):337-341 829
Demchuk E, Mueller T, Oschkinat H, Sebald W, Wade RC (1994). Receptor binding properties of four-helix-bundle growth factors deduced from electrostatic analysis, Protein Science 3(6):920-935 830
Pisabarro MT, Ortiz AR, Serrano L, Wade RC (1994). Homology Modeling of the Abl-SH3 domain, Proteins 20(3):203-215 831

1993

Luty BA, Wade RC, Madura JD, Davis ME, Briggs JM, McCammon JA (1993). Brownian Dynamics Simulations of Diffusional Encounters between Triose Phosphate Isomerase and Glyceraldhyde Phosphate: Electrostatic Steering of Glyceraldehyde Phosphate, J. Phys. Chem. 97(1):233-237 832
Wade R, Davis M, Luty B, Madura J, McCammon J (1993). Gating of the Active Site of Triose Phosphate Isomerase: Brownian Dynamics Simulations of Flexible Peptide Loops in the Enzyme, Biophysical Journal 64(1):9-15 833
Wade RC, Clark KJ, Goodford PJ (1993). 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, J. Med. Chem. 36(1):140-147 834
Wade RC, Goodford PJ (1993). 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, J. Med. Chem. 36(1):148-156 835
Demchuk E, Vihinen M, Wade R, Korpela T (1993). Modeling three-dimensional structure and electrostatics of alkali-stable cyclomaltodextrin glucanotransferase, In Stability and Stabilization of Enzymes, pp. pp291–298, Eds. van der Tweel,W.J.J.; Harder,A. and Buitelaar,R.M. Elsevier, Netherlands 836
Wade R, Bohr H, Wolynes P (1993). Use of neural networks to predict hydration sites in proteins, In Trends in QSAR and Molecular Modelling ’92, pp. pp396–397, Ed. Wermuth,C.G. ESCOM, Leiden 837
Wade R (1993). Molecular Interaction Fields, In 3D QSAR in Drug Design. Theory, Methods and Applications, pp. pp486–505, Ed. Kubinyi,H. ESCOM, Leiden 838

1992

Wade RC, McCammon J (1992). 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, Journal of Molecular Biology 225(3):679-696 839
Wade RC, McCammon J (1992). 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, Journal of Molecular Biology 225(3):697-712 840
Wade RC, Bohr H, Wolynes PG (1992). Prediction of Water Binding Sites on Proteins by Neural Networks, J. Am. Chem. Soc. 114(21):8284-8285 841

1991

Wade RC, Mazor MH, McCammon JA, Quiocho FA (1991). A Molecular Dynamics Study of Thermodynamic and Structural Aspects of the Hydration of Cavities in Proteins, Biopolymers 31(8):919-931 842

1990

Wade R (1990). An Approach to the Design of Anti-Influenza Agents, In Use of X-Ray Crystallography in the Design of Antiviral Agents, pp. pp61–74, Eds. Laver,G. and Air,G. Academic Press, Inc., San Diego 843
Wade RC (1990). Solvation of the Active Site of Cytochrome P450-cam, J Computer-Aided Mol Des 4(2):199-204 844
Wade RC, Mazor MH, McCammon JA, Quiocho FA (1990). Hydration of Cavities in Proteins: a Molecular Dynamics Approach, J. Am. Chem. Soc. 112(19):7057-7059 845

1989

Wade R, Goodford P (1989). The Role of Hydrogen-bonds in Drug Binding, In Prog. Clin. Biol. Res., pp. pp433–444, Ed. Golombek,A., Alan R. Liss, Inc., New York 846
Boobbyer DNA, Goodford PJ, McWhinnie PM, Wade RC (1989). New Hydrogen-bond Potentials for Use in Determining Energetically Favourable Binding Sites on Molecules of Known Structure, J. Med. Chem. 32(5):1083-1094 847
Reynolds CA, Wade RC, Goodford PJ (1989). Identifying Targets for Bioreductive Agents, Journal of Molecular Graphics 7(2):103-108 848

1988

Wade R, Goodford P (1988). The Use of Molecular Graphics in the Design of Anti-influenza Agents, Br. J. Pharmac. Proc. Suppl. 95:588P 849

2025

Muñiz‐Chicharro A (2025). Prediction of drug-protein binding kinetics (Doctoral Thesis), Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 2057
Prediction of Binding Kinetics of the Interleukin-13-Interleukin-13 Receptor alpha1 Complex (Master’s Thesis), Molecular Biosciences, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 2059

2024

Structural bioinformatics approach to exploring transient binding pockets in proteins (Bachelor’s Thesis), Faculty of Biosciences and Faculty of Chemistry and Earth Sciences, Ruprecht-Karls University, Heidelberg 1899
Structural bioinformatics approach to exploring transient binding pockets in proteins, (Bachelor’s Thesis), Biochemistry, Faculty of Biosciences and Faculty of Chemistry and Earth Sciences, Ruprecht-Karls University, Heidelberg (Bachelor’s Thesis) 1874
Investigation of the impact of mutations in Cytochrome P450 reductase on the rate of electron transfer to Cytochrome P450 by molecular dynamics simulations (Master’s Thesis), Chemistry, Department of Chemistry, Ruprecht-Karls University, Heidelberg 1898

2023

Nießner J (2023). Computational Models of Hen Egg White Lysozyme Physisorption to Silica- and Mica-like Surfaces (Master’s Thesis), Physics, Department of Physics and Astronomy, Ruprecht-Karls University, Heidelberg 1759
Athanasiou C (2023). Modeling of mechanistic effects of neurotrophin modulators (Doctoral Thesis), Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1760
Tarnow M (2023). Optimization of a Drug: Polymer Formulation Exploiting a Computational Approach based on Molecular Dynamics Simulations (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Engineering Sciences, Ruprecht-Karls University, Heidelberg 1762
Ferraz M (2023). Enhanced sampling simulations and machine learning to address infectious diseases (Doctoral Thesis), Chemistry, Department of Chemistry, Federal University of Pernambuco, Recife, Brazil 1785

2022

Kaeser M (2022). Computational Investigation of the Structure Kinetics Relationship of Small-Molecule Compounds Binding the Histamine-1-Receptor (Master’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1582
Teuffel J (2022). Molecular Dynamics Simulation of a Mammalian Cytochrome P450 Protein and its Interaction with Substrates and Redox-Partners (Master’s Thesis), Biochemistry, Faculty of Biosciences and Faculty of Chemistry and Earth Sciences, Ruprecht-Karls University, Heidelberg 1445
Emmert M (2022). Generation and Testing of Boltzmann Generators Trained on Peptide Molecular Dynamics Simulations to Predict Peptide Conformational Behaviour (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1579
Hanke A (2022). P. falciparum Circumsporozoite protein epitope/paratope interactions: Addressing the key role of molecular flexibility (Master’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1580
Cabezudo AC (2022). Structural Insights into Neurotrophin Receptor Dimerization using Coarse-grained Molecular Dynamics Simulations (Master’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1581

2021

Dohrke J (2021). Molecular mechanisms of AMPAR modulation by auxiliary subunits (Master’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1207
Marinis PD (2021). Assessing ML-database augmentation approaches for Druggability Score calculations in TRAPP-pocket (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1441
Messner L (2021). Comparison of ligand docking to the AMPAR-TARP interaction site between different isoforms (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg, 2021 1442
Han SB (2021). Multi-Resolution Simulation Study of CYP 2B4 to Investigate Complex Formation with Human NADPH-Cytochrome P450 Oxidoreductase in Lipid Bilayer (Master’s Thesis), Molecular Biosciences, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1443
De M (2021). The effects of the linker-DNA on linker histone positioning: a single-pair FRET study from mono to trichromatosomes (Doctoral Thesis), Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University, Heidelberg 1444

2020

Ormersbach F (2020). Computational ligand superimposition and analysis of protein-ligand interaction fingerprints (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1204
Jarosch L (2020). Computational modeling of SERCA interactions with S100A1ct and DWORF fingerprints (Bachelor’s Thesis), Biochemistry, Faculty of Biosciences and Faculty of Chemistry and Geosciences, Ruprecht-Karls University, Heidelberg 1205
Pöhner IA (2020). Computational approaches to drug design against the folate & biopterin pathways of parasites causing neglected tropical diseases (Doctoral Thesis), Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University, Heidelberg 1206

2019

Hanke A (2019). Computational characterisation of protein homo- and heterodimer formation (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1010
Ullmann P (2019). Molecular dynamics simulation studies of gp41 cytoplasmic tail lateral embedding in phospholipid bilayer (Bachelor’s Thesis), Biosciences, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1011
Yuan J (2019). Druggability Assessment in TRAPP Procedure using Machine Learning Approaches (Master’s Thesis), Master of Scientific Computing, Fakultät für Mathematik und Informatik, Ruprecht-Karls University, Heidelberg 1012
Ganotra GK (2019). Computational studies of drug-binding kinetics (Doctoral Thesis), Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University, Heidelberg 1013

2018

Friedrich P (2018). A novel method to treat gated protein-ligand binding via on-the-fly conformational updates within rigid body BD simulations (Master’s Thesis), Faculty of Physics, Ruprecht-Karls University Heidelberg 880
Öztuerk MA (2018). A computational approach to decipher chromatosome structure determinants (Doctoral Thesis), Combined Faculties of the Natural Sciences and for Mathematics, Ruprecht-Karls University Heidelberg 882
Dohrke J (2018). Modelling of Neurotrophin Receptors (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg 1032

2017

Reinhardt M (2017). Development of Hydrodynamic Coarse-Grain Models for Brownian Dynamics Simulations of Crowded Protein Systems (Master’s Thesis), Faculty of Physics, Ruprecht-Karls University Heidelberg 877
Mustafa G (2017). Modeling and Simulation of Membrane Proteins to Understand their Structure, Dynamics and Function (Doctoral Thesis), Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University Heidelberg 878
Stank A (2017). Computational Studies on the Relation Between Macromolecular Dynamics and Protein Binding and Function. (Doctoral Thesis), Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University Heidelberg 879
Buerkel C (2017). Towards development of Random Acceleration Molecular Dynamics simulation analysis software for predicting drug residence time (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg 1031

2016

Ozboyaci M (2016). Modeling and Simulation of Protein-Surface Interactions (Doctoral Thesis), Combined Faculty for the Natural Sciences and Mathematics, Ruprecht-Karls University Heidelberg 876
Stubbusch A (2016). Case Study of Human Growth Hormone Interactions by Brownian Dynamics Simulation (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg 1030

2015

Berinski M (2015). Macromolecular Interactions: in silico prediction of the structures of complexes between proteins (Doctoral Thesis), Faculty of Informatics and Mathematics, Johann Wolfgang Goethe Universität, Frankfurt am Main 883
Ganotra GK (2015). Methods to Compute and Investigate Drug Binding Kinetics (Master’s Thesis), Life Science Informatics, University of Bonn 884
Yu X (2015). Multiscale Simulations of Cytochrome P450 Systems (Doctoral Thesis), Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg 885
Horn M (2015). Clustering and Scoring the Druggability of Transient Protein Pockets (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg 1028
Waldhauer M (2015). Brownian Dynamics Simulations of Chymotrypsin Inhibitor 2 in Concentrated Protein Solutions (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University Heidelberg 1029

2014

Tong R (2014). Comparative analysis of Adenylyl Cyclase binding sites (Bachelor’s Thesis), Molecular Biotechnology, Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 1027

2013

Banerjee P (2013). An Algorithmic Approach to Peptidomimetics (Master’s Thesis), Masters Programme in Life Science Informatics, Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn 852

2012

Monninger T (2012). Dynamische hybride Cloud für wissenschaftliche Anwendungen (Master’s Thesis), Fakultaet fuer Mathematik und Informatik, Ruprecht-Karls University, Heidelberg 853

2011

Subramaniam SR (2011). Sequence, Structure and Stability of Collagen and its Interaction with Collagenase. (Doctoral Thesis), University of Madras, Chennai. 854
Garg D (2011). Computational and NMR Studies of Thymidylate Synthase and its Regulation (Doctoral Thesis), Faculty of Chemistry, Technical University of Munich 855
Veith N (2011). Structural Comparison of Pyruvate Kinases. (Master’s Thesis), Faculty of Biosciences, Ruprecht-Karls University, Heidelberg 856
Nerini E (2011). System Approach to the Identification of Folate-related Enzyme Inhibitors with Anti-infectious Action (Doctoral Thesis), Doctoral School of Science and Technologies for Health Products, University of Modena and Reggio Emilia 857

2010

Feldman-Salit A (2010). Computation and Modeling of Molecular Recognition: The Cysteine Synthase Complex (Doctoral Thesis), Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University of Heidelberg 858

2009

Pachov GV (2009). Linker Histone-Nucleosome Interactions: A Modelling and Simulation Study (Doctoral Thesis), Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University,Heidelberg 859
Berynskyy M (2009). Automatisierte Analyse von Brownian Dynamics Simulationen (Master’s Thesis), Bioinformatics, Giessen-Friedberg University of Applied Sciences 860

2007

Motiejunas D (2007). Modeling of macromolecular interactions (Doctoral Thesis), Combined Faculties of the Natural Sciences and for Mathematics, Ruperto-Carola University, Heidelberg 861

2006

Zahran M (2006). 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’s Thesis), Bioinformatics, University Paris VII 862

2005

Besson B (2005). Development of a software to aid the search of protein structural information to estimate kinetic parameters in systems biology applications (Master’s Thesis), Bioinformatics and Modeling, National Institute of Applied Science (INSA) Lyon 863
Johann TI (2005). Perturbation Methods in Molecular Dynamics Simulations with Implicit Solvent Models (Diplom Thesis), Physics, Ruperto-Carola University, Heidelberg 1014

2004

Motiejunas D (2004). Protein-protein docking assisted by sequence conservation and experimental data (Master’s Thesis), Molecular Biology, Ruperto-Carola University,Heidelberg 864
R.Hallingbaeck H (2004). Peroxidases: A computational study of ligand binding and enzyme kinetics (Master’s Thesis), Molecular Biotechnology, Uppsala University School of Engineering, Uppsala 865

2003

Doudieu OMN (2003). Using Sequence Information in Protein Docking Procedures (Master’s Thesis), Bioinformatics, University of Applied Sciences, Berlin 866
Battey JN (2003). High-throughput Structural and Electrostatic Modelling of Ubiquitin Conjugating Enzymes (Master’s Thesis), Bioinformatics, Exeter University, Exeter 867
Pulagam LVP (2003). Structure-based design of inhibitors of enzymes of the ubiquitin mediated protein degradation pathway (Master’s Thesis), Bioinformatics, Cologne University Bioinformatics Center, University of Cologne 868
Neumann GF (2003). Entwicklung einer erweiterten Anwendung der Hauptkomponentenanalyse fuer das Protein-Protein Dockingproblem (Diplom Thesis), Physics, Ruperto-Carola University, Heidelberg 1015

2001

Ferrari S (2001). Inhibition studies of enzymes involved in drug resistance phenomena. Library-design and Structure-based approaches towards species-specific inhibitors of Thymidylate Synthase (Doctoral Thesis), University of Modena and Reggio Emilia, Modena 869
Gonzalez A (2001). Glycolytic Pathway Reaction Animations (Diplom Thesis), Biology, Ruperto-Carola University, Heidelberg 1016

1999

Nardi F (1999). Molecular Dynamics and NMR Spectroscopic Studies of Local Interactions of Small Peptides in Aqueous Solution Involving Aromatic Residues (Doctoral Thesis), Universite Joseph Fourier, Grenoble 870
Rienzo FD (1999). Computational studies of blue copper proteins (Doctoral Thesis), University of Modena and Reggio Emilia, Modena 871
Koboyashi M (1999). Chloride ion exchange routes in Haloalkane Dehalogenase from Xanthobacter autrophicus detected by Thermal Motion Pathway analysis, GRID and Essential Dynamics (Master’s Thesis), University of York 872
Gauges R (1999). Molekulardynamische Simulation zur Aufklaerung des Substratzuganges in Cytochrom P450eryF (Diplom Thesis), Biology, Eberhard-Karls University, Tubingen 1017

1998

Bitomsky W (1998). Binding of Glycosaminoglycans to Heparin-Binding Proteins (Doctoral Thesis), University of Vienna 873

1996

Ortiz AR (1996). Rational design of Human Synovial Fluid Phospholipase A2 inhibitors and analysis of their three-dimensional structure-activity relationships (Doctoral Thesis), University of Alcala de Henares, Madrid 874
Helms V (1996). Hydratation des aktiven Zentrums von Cytochrom P450cam – Untersuchung mit Molekueldynamik-Simulationen (Doctoral Thesis), Ludwig-Maximilians University, Munich 875
Reimer N (1996). Dynamische Einstellung des Parallelitaetsgrades mit reflexiven Programmen (Diplom Thesis), Computer Science, University of Karlsruhe, Tubingen 1018

1995

Degenhardt M (1995). De-Novo Design von Liganden zur Blockierung der Substratzugaenlichkeit von Cytochrom P450cam (Diplom Thesis), Biology, Ruperto-Carola University, Heidelberg 1019

1988

Wade R (1988). Ligand-Macromolecule Interactions (Doctoral Thesis), University of Oxford 850

2013

Costi MP, Luciani R, Nerini E, D. G, Ferrari S, Venturelli A, Lazzari S, Wade RC, Henrich S, Motiejunas D (2013). Uso di inhibitori della Pteridina Reduttasi per la prevenzione e/o il trattamento di infezioni parassitarie, Italian Patent Nr. 1403584, Date of Patent: 31.10.2013, Filed : 25.11.2010 1034

2009

Costi MP, Marverti G, Cardinale D, Venturelli A, Ferrari S, Ponterini G, Henrich S, Salo-Ahen O, Wade RC (2009). Peptides binding to the dimer interface of thymidylate synthase for the treatment of cancer, United States Patent No.: US 8,916,679 B2, Date of Patent: 23.12.2014. Filed: 17.08.2012, 01.12.2009 1033