Molecular and Cellular Modeling Molecular recognition, binding and catalysis are fundamental processes in cell function. The ability to understand how macromolecules interact with their binding partners and participate in complex cellular networks is crucial to prediction of macromolecular function, and to applications such as protein engineering and structure-based drug design. Original Papers 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 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,S2451945621000039 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 4:55 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 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 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 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 Plasmodium actin filaments, PLoS Biol 16(7):e2005345 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 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 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
Reviews 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 Öztürk MA, De M, Cojocaru V, Wade RC (2020). Chromatosome Structure and Dynamics from Molecular Simulations, Annu. Rev. Phys. Chem. 71(1):101-119 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 Stank A, Kokh DB, Fuller JC, Wade RC (2016). Protein Binding Pocket Dynamics, Acc. Chem. Res. 49(5):809-815 Ozboyaci M, Kokh DB, Corni S, Wade RC (2016). Modeling and simulation of protein–surface interactions: achievements and challenges, Quart. Rev. Biophys. 49,e4 |
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