Prof. Dr. Rebecca Wade

2021

• 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
• 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

2020

• 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
• 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
• 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

• Petit V, Wade G, Schneider F, Foßati L, Kamp K, Neiner C, David-Uraz A, Alecian E, Collaboration M (2019). The MiMeS survey of magnetism in massive stars: magnetic properties of the O-type star population, Monthly Notices of the Royal Astronomical Society 489(4):5669-5687 1062
• 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
• 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
• 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 R, 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
• 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
• 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
• 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
• 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
• 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
• 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 89(2) 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
• 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
• 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
• Ros 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
• 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
• 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

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
• 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
• 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
• 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
• 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
• 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

2009

• 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
• 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
• 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
• 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
• 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
• Henrich S, Richter S, Wade R (2008). On the use of PIPSA to Guide Target-Selective Drug Design, ChemMedChem 3(3):413-417 635
• 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
• 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

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

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

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