The Elcock group is a combined computational-and-experimental group that focuses on applying molecular simulation methods to understand biochemical and biological phenomena. Members of the group have a broad range of backgrounds (from protein expression to theoretical physics) and include undergraduates, graduate students and post-docs. Our current research falls into three main areas:
1.Developing Brownian Dynamics (BD) methods to simulate very large, complex macromolecular systems. This work involves modeling protein diffusion, association and folding events, etc. The software used to conduct our work in this area is a version, heavily modified by AHE, of the BD simulation code SDA.
2.Applying Molecular Dynamics (MD) methods to study the thermodynamics and kinetics of biomolecular associations. This work is more chemical in nature; it aims at obtaining fundamental insights into the nature of molecular interactions, focusing on electrostatic and hydrophobically-driven associations. Our simulations in this area are typically conducted with the MD software package GROMACS.
3.Studying the interactions between small-molecule inhibitors and protein kinases. This work involves a combination of computational and experimental efforts: we are using Isothermal Titration Calorimetry (ITC) and X-ray crystallography to examine how modest mutations in a protein kinase affect the binding of ATP-competitive inhibitors. At the same time, we are using free energy simulations to assess whether current computational techniques can successfully ‘predict’ the observed structural and thermodynamic changes.