A glycan gate controls opening of the SARS-CoV-2 spike protein
Sztain, Terra, Ahn, Surl-Hee, Bogetti, Anthony T., Casalino, Lorenzo, Goldsmith, Jory A., Seitz, Evan, McCool, Ryan S., Kearns, Fiona L., Acosta-Reyes, Francisco, Maji, Suvrajit, Mashayekhi, Ghoncheh, McCammon, J. Andrew, Ourmazd, Abbas, Frank, Joachim, McLellan, Jason S., Chong, Lillian T., Amaro, Rommie E.
Published in Nature chemistry (01.10.2021)
Published in Nature chemistry (01.10.2021)
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AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics
Casalino, Lorenzo, Dommer, Abigail C, Gaieb, Zied, Barros, Emilia P, Sztain, Terra, Ahn, Surl-Hee, Trifan, Anda, Brace, Alexander, Bogetti, Anthony T, Clyde, Austin, Ma, Heng, Lee, Hyungro, Turilli, Matteo, Khalid, Syma, Chong, Lillian T, Simmerling, Carlos, Hardy, David J, Maia, Julio DC, Phillips, James C, Kurth, Thorsten, Stern, Abraham C, Huang, Lei, McCalpin, John D, Tatineni, Mahidhar, Gibbs, Tom, Stone, John E, Jha, Shantenu, Ramanathan, Arvind, Amaro, Rommie E
Published in The international journal of high performance computing applications (01.09.2021)
Published in The international journal of high performance computing applications (01.09.2021)
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Journal Article
The RED scheme: Rate-constant estimation from pre-steady state weighted ensemble simulations
DeGrave, Alex J, Bogetti, Anthony T, Chong, Lillian T
Published in The Journal of chemical physics (21.03.2021)
Published in The Journal of chemical physics (21.03.2021)
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Journal Article
WatFinder: a ProDy tool for protein–water interactions
Krieger, James M, Doljanin, Frane, Bogetti, Anthony T, Zhang, Feng, Manivarma, Thiliban, Bahar, Ivet, Mikulska-Ruminska, Karolina
Published in Bioinformatics (Oxford, England) (02.08.2024)
Published in Bioinformatics (Oxford, England) (02.08.2024)
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LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways
Bogetti, Anthony T., Leung, Jeremy M. G., Chong, Lillian T.
Published in Journal of chemical information and modeling (25.12.2023)
Published in Journal of chemical information and modeling (25.12.2023)
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Journal Article
The Next Frontier for Designing Switchable Proteins: Rational Enhancement of Kinetics
Bogetti, Anthony T, Presti, Maria F, Loh, Stewart N, Chong, Lillian T
Published in The journal of physical chemistry. B (19.08.2021)
Published in The journal of physical chemistry. B (19.08.2021)
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Journal Article
Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories
Zhang, She, Thompson, Jeff P, Xia, Junchao, Bogetti, Anthony T, York, Forrest, Skillman, A. Geoffrey, Chong, Lillian T, LeBard, David N
Published in Journal of chemical information and modeling (25.04.2022)
Published in Journal of chemical information and modeling (25.04.2022)
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Journal Article
WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications
Russo, John D, Zhang, She, Leung, Jeremy M G, Bogetti, Anthony T, Thompson, Jeff P, DeGrave, Alex J, Torrillo, Paul A, Pratt, A J, Wong, Kim F, Xia, Junchao, Copperman, Jeremy, Adelman, Joshua L, Zwier, Matthew C, LeBard, David N, Zuckerman, Daniel M, Chong, Lillian T
Published in Journal of chemical theory and computation (08.02.2022)
Published in Journal of chemical theory and computation (08.02.2022)
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Journal Article
A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics
Bogetti, Anthony T, Piston, Hannah E, Leung, Jeremy M G, Cabalteja, Chino C, Yang, Darian T, DeGrave, Alex J, Debiec, Karl T, Cerutti, David S, Case, David A, Horne, W Seth, Chong, Lillian T
Published in The Journal of chemical physics (14.08.2020)
Published in The Journal of chemical physics (14.08.2020)
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Journal Article
A glycan gate controls opening of the SARS-CoV-2 spike protein
Sztain, Terra, Ahn, Surl-Hee, Bogetti, Anthony T, Casalino, Lorenzo, Goldsmith, Jory A, Seitz, Evan, McCool, Ryan S, Kearns, Fiona L, Acosta-Reyes, Francisco, Maji, Suvrajit, Mashayekhi, Ghoncheh, McCammon, J Andrew, Ourmazd, Abbas, Frank, Joachim, McLellan, Jason S, Chong, Lillian T, Amaro, Rommie E
Published in bioRxiv (17.05.2021)
Published in bioRxiv (17.05.2021)
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Paper
A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0]
Bogetti, Anthony T, Mostofian, Barmak, Dickson, Alex, Pratt, A J, Saglam, Ali S, Harrison, Page O, Adelman, Joshua L, Dudek, Max, Torrillo, Paul A, DeGrave, Alex J, Adhikari, Upendra, Zwier, Matthew C, Zuckerman, Daniel M, Chong, Lillian T
Published in Living journal of computational molecular science (2019)
Published in Living journal of computational molecular science (2019)
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Journal Article
A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]
Bogetti, Anthony T, Leung, Jeremy M G, Russo, John D, Zhang, She, Thompson, Jeff P, Saglam, Ali S, Ray, Dhiman, Mostofian, Barmak, Pratt, A J, Abraham, Rhea C, Harrison, Page O, Dudek, Max, Torrillo, Paul A, DeGrave, Alex J, Adhikari, Upendra, Faeder, James R, Andricioaei, Ioan, Adelman, Joshua L, Zwier, Matthew C, LeBard, David N, Zuckerman, Daniel M, Chong, Lillian T
Published in Living journal of computational molecular science (2023)
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Published in Living journal of computational molecular science (2023)
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