Rebecca Wade Molecular & 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. The Molecular and Cellular Modeling (MCM) group works on the development and application of computer-aided methods to predict and simulate biomolecular interactions. The focus is on proteins and our computational approaches are mostly based on the three-dimensional structures of macromolecules. Techniques cover a wide spectrum from interactive, web-based visualization tools to molecular and Brownian dynamics simulations.
Recent Research Highlights
Current Research
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.
The Molecular and Cellular Modeling (MCM) group works on the development and application of computer-aided methods to predict and simulate biomolecular interactions. The focus is on proteins and our computational approaches are mostly based on the three-dimensional structures of macromolecules. Techniques cover a wide spectrum from interactive, web-based visualization tools to molecular and Brownian dynamics simulations.
5 Selected publications
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