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Lillian Chong

University of Pittsburgh
Ph.D., Biophysics, University of California San Francisco, 2002

Lillian Chong received her B.S. in Chemistry from MIT and went on to pursue a Ph.D. in Biophysics at the University of California San Francisco. She is now an associate professor of Chemistry at the University of Pittsburgh and holds a secondary appointment in Computational & Systems Biology. She is also involved in two joint CMU-Pitt programs, one in Computational Biology and the other in Molecular Biophysics/Structural Biology. She has won several awards, among which the NSF-CAREER award in 2009 and the very select Chinese American Chemical Society Scholar award during her undergraduate studies.


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, 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.


Title Position Email
Andrew Bellesis Graduate Student
Anthony Bogetti Graduate Student
Karl Debiec Graduate Student
Max Dudek Undergraduate Student
Corinn Durham Graduate Student
Page Harrison Undergraduate Student
Audrey Pratt Graduate Student
Ali Saglam Graduate Student
Most Cited Publications

"Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models"  Kollman, P.A., Massova, I., Reyes, C., (...), Case, D.A., Cheatham III., T.E. Accounts of Chemical Research
"The Amber biomolecular simulation programs" Case, D.A., Cheatham III, T.E., Darden, T., (...), Wang, B., Woods, R.J. Journal of Computational Chemistry 26(16), pp. 1668-1688
"GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit" Kollman, P.A., Massova, I., Reyes, C., (...), Case, D.A., Cheatham III., T.E. Accounts of Chemical Research
"Docking and scoring in virtual screening for drug discovery: Methods and applications" Kitchen, D.B., Decornez, H., Furr, J.R., Bajorath, J. 2004 Nature Reviews Drug Discovery
"Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model" Onufriev, A., Bashford, D., Case, D.A. Proteins: Structure, Function and Genetics

Recent Publications

"Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields,"  K T Debiec, A M Gronenborn, and L T Chong.  Journal of Physical Chemistry B 123.19 (2019)

"Large enhancement of response times of a protein conformational switch by computational design,"  Alex J. DeGrave, Jeung-Hoi Ha, Stewart N. Loh & Lillian T. Chong, Nature Commnications, 9, 1013 (2018).

"Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein." Debiec, K.T., Whitley, M.J., Koharudin, L.M.I., Chong, L.T., Gronenborn, A.M.     Biophysical Journal 114(4), pp. 839-855. (2018).

"WESTPA 2.0 Advances in Sampling, Storage, and Analysis of Weighted Ensemble Simulations,"  AJ Pratt, D M Zuckerman, and L T Chong.  Biophysical Journal 114.3 (2018)

"Links between the charge model and bonded parameter force constants in biomolecular force fields." Cerutti, D.S., Debiec, K.T., Case, D.A., Chong, L.T.     Journal of Chemical Physics 147(16),161730. (2017).