Our research is focused on the use of molecular simulations to characterize the free energy landscapes and kinetics of a variety of biological processes, including large protein conformational transitions and protein binding. We have also been developing simulation strategies for aiding the design of protein-based conformational switches. Finally, we are developers of an upcoming AMBER force field and https://westpa.github.io/westpa/, a freely available, highly scalable software implementation of weighted ensemble path sampling strategies for the simulation of rare events (e.g. protein folding and protein binding).
Our research falls into the following main areas:
1) Development of weighted ensemble path sampling strategies and software for the efficient sampling of rare events (e.g. protein folding and binding) with rigorous kinetics.
2) Application of molecular simulations to investigate the mechanisms of protein conformational transitions, binding, and assembly processes.
3) Development of molecular simulation strategies for aiding the design of protein conformational switches.
4) Development of biomolecular force fields.
- "Weighted Ensemble Simulation: Review of Methodology, Applications, and Software (Review)," Zuckerman, D.M., Chong, L.T., Annual Review of Biophysics 46, 43 (2017)
- "Path-sampling strategies for simulating rare events in biomolecular systems," Chong, L.T., Saglam, A.S., Zuckerman, D.M., Current Opinion in Structural Biology 43, 88, (2017)
- "Efficient Atomistic Simulation of Pathways and Calculation of Rate Constants for a Protein-Peptide Binding Process: Application to the MDM2 Protein and an Intrinsically Disordered p53 Peptide," Zwier, M.C., Pratt, A.J., Adelman, J.L., Kaus, J.W., Zuckerman, D.M., Chong, L.T., J. Phys. Chem. Lett 7, 3440 (2016)
- "Further along the Road Less Traveled: AMBER ff15ipq, an Original Protein Force Field Built on a Self-Consistent Physical Model," Debiec, K.T., Cerutti, D.S., Baker, L.R., Gronenborn, A.M., Case, D.A., Chong, L.T., J. Chem. Theory Comput. 12, 3926 (2016)
- "Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models," Saglam, A.S., Chong, L.T., J. Phys. Chem. B 120, 117 (2016)