Author
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
10 papers
Recent·Most cited
A. Bogetti, J. M. Leung, L. Chong
The paper introduces LPATH, a Python tool for clustering molecular pathways using linguistics-assisted methods, demonstrating its effectiveness on alanine dipeptide conformational transitions.
bioRxiv · Aug 17, 2023 · PreprintBiophysics
A. M. Xu, A. Jiang, T. Aoki, A. Gamboa, L. Chong, A. R. Colombo, Y. Yin, J. Lownik, K. Takata, M. Hav, C. Steidl, A. Merchant
This study uses spatial imaging to analyze Hodgkin lymphoma tumor microenvironments and identifies new biomarkers related to immune cell interactions and checkpoints.
bioRxiv · May 24, 2023 · PreprintCancer Biology
A. Bogetti, J. Leung, J. Russo, S. Zhang, J. Thompson, A. Saglam, D. Ray, R. Abraham, J. Faeder, I. Andricioaei, J. Adelman, M. Zwier, D. LeBard, D. M. Zuckerman, L. Chong
The paper provides advanced tutorials for WESTPA 2.0, demonstrating new features for rare-events sampling in molecular simulations.
bioRxiv · Oct 4, 2022 · PreprintBiophysics
D. Yang, A. Gronenborn, L. Chong
The paper develops and validates force field parameters for fluorinated amino acids in the AMBER ff15ipq force field, enabling accurate MD simulations of fluorinated proteins and validating them with experimental NMR data.
bioRxiv · Jan 6, 2022 · PreprintBiophysics
J. Russo, S. Zhang, J. Leung, A. Bogetti, J. Thompson, A. DeGrave, P. Torrillo, A. J. Pratt, K. Wong, J. Xia, J. T. Copperman, J. Adelman, M. Zwier, D. LeBard, D. M. Zuckerman, L. Chong
The paper introduces WESTPA 2.0, an upgraded software package for weighted ensemble simulations, enhancing efficiency and analysis of longer-timescale applications.
bioRxiv · Dec 5, 2021Biophysics
T. E. Sztain, S.-H. Ahn, A. T. Bogetti, L. Casalino, J. A. Goldsmith, E. Seitz, R. S. McCool, F. L. Kearns, F. Acosta-Reyes, S. Maji, G. Mashayekhi, J. A. McCammon, A. Ourmazd, J. Frank, J. S. McLellan, , R. E. Amaro
This study identifies a glycan gate and key residues that facilitate SARS-CoV-2 spike protein RBD opening through simulations and experimental validation.
bioRxiv · Feb 15, 2021Biophysics
L. Casalino, A. C. Dommer, Z. Gaieb, E. P. Barros, T. Sztain, S.-H. Ahn, A. Trifan, A. Brace, H. Ma, H. Lee, M. Turilli, A. Bogetti, S. Khalid, L. Chong, C. Simmerling, , R. E. Amaro
This paper develops an AI-driven workflow to simulate SARS-CoV-2 spike protein dynamics, revealing glycan shield structure, spike glycans' role in infectivity, and spike-ACE2 interactions.
bioRxiv · Nov 19, 2020Biophysics
P. A. Torrillo, A. T. Bogetti, L. Chong
This paper introduces a minimal adaptive binning scheme for weighted ensemble simulations, showing it is more efficient than fixed binning in sampling rare events and estimating rate constants.
bioRxiv · Nov 5, 2020Biophysics
A. Pratt, E. Suarez, D. Zuckerman, L. Chong
This study evaluates weighted ensemble strategies for calculating molecular association/dissociation rate constants and binding affinities, finding that heavy-weight simulations are most efficient when states are predefined.
bioRxiv · Jun 14, 2019 · PreprintBiophysics
The paper uses weighted ensemble simulations to study protein-protein binding pathways, finding that the encounter complex formation is rate-limiting and identifying key residues and water molecules involved.
bioRxiv · Oct 26, 2018Biophysics