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WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.
J Chem Theory Comput. 2022 Feb 8;18(2):638-649. doi: 10.1021/acs.jctc.1c01154. Epub 2022 Jan 19.
J Chem Theory Comput. 2022.
PMID: 35043623
Free PMC article.
A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics.
Bogetti AT, Piston HE, Leung JMG, Cabalteja CC, Yang DT, DeGrave AJ, Debiec KT, Cerutti DS, Case DA, Horne WS, Chong LT.
Bogetti AT, et al. Among authors: leung jmg.
J Chem Phys. 2020 Aug 14;153(6):064101. doi: 10.1063/5.0019054.
J Chem Phys. 2020.
PMID: 35287464
Free PMC article.
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Implications of the unfolded state in the folding energetics of heterogeneous-backbone protein mimetics.
Santhouse JR, Leung JMG, Chong LT, Horne WS.
Santhouse JR, et al. Among authors: leung jmg.
Chem Sci. 2022 Sep 20;13(40):11798-11806. doi: 10.1039/d2sc04427g. eCollection 2022 Oct 19.
Chem Sci. 2022.
PMID: 36320921
Free PMC article.
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A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].
Bogetti AT, Leung JMG, Russo JD, Zhang S, Thompson JP, Saglam AS, Ray D, Mostofian B, Pratt AJ, Abraham RC, Harrison PO, Dudek M, Torrillo PA, DeGrave AJ, Adhikari U, Faeder JR, Andricioaei I, Adelman JL, Zwier MC, LeBard DN, Zuckerman DM, Chong LT.
Bogetti AT, et al. Among authors: leung jmg.
Living J Comput Mol Sci. 2023;5(1):1655. doi: 10.33011/livecoms.5.1.1655.
Living J Comput Mol Sci. 2023.
PMID: 37200895
Free PMC article.
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LPATH: A semi-automated Python tool for clustering molecular pathways.
Bogetti AT, Leung JMG, Chong LT.
Bogetti AT, et al. Among authors: leung jmg.
bioRxiv [Preprint]. 2023 Oct 19:2023.08.17.553774. doi: 10.1101/2023.08.17.553774.
bioRxiv. 2023.
PMID: 37645995
Free PMC article.
Updated.
Preprint.
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LPATH: A Semiautomated Python Tool for Clustering Molecular Pathways.
Bogetti AT, Leung JMG, Chong LT.
Bogetti AT, et al. Among authors: leung jmg.
J Chem Inf Model. 2023 Dec 25;63(24):7610-7616. doi: 10.1021/acs.jcim.3c01318. Epub 2023 Dec 4.
J Chem Inf Model. 2023.
PMID: 38048485
Free PMC article.
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Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein.
Santhouse JR, Leung JMG, Chong LT, Horne WS.
Santhouse JR, et al. Among authors: leung jmg.
Chem Sci. 2023 Dec 4;15(2):675-682. doi: 10.1039/d3sc03976e. eCollection 2024 Jan 3.
Chem Sci. 2023.
PMID: 38179541
Free PMC article.
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