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For: Suárez E, Pratt AJ, Chong LT, Zuckerman DM. Estimating first-passage time distributions from weighted ensemble simulations and non-Markovian analyses. Protein Sci 2016;25:67-78. [PMID: 26131764 PMCID: PMC4815309 DOI: 10.1002/pro.2738] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 01/17/2023]
Number Cited by Other Article(s)
1
Ono J, Matsumura Y, Mori T, Saito S. Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events. J Phys Chem B 2024;128:20-32. [PMID: 38133567 DOI: 10.1021/acs.jpcb.3c05307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
2
Yeh CY, Izaguirre JA, Greisman JB, Willmore L, Maragakis P, Shaw DE. A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. J Chem Inf Model 2023. [PMID: 37378552 DOI: 10.1021/acs.jcim.3c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
3
Spiriti J, Noé F, Wong CF. Simulation of ligand dissociation kinetics from the protein kinase PYK2. J Comput Chem 2022;43:1911-1922. [PMID: 36073605 PMCID: PMC9976590 DOI: 10.1002/jcc.26991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/11/2022] [Accepted: 08/03/2022] [Indexed: 11/09/2022]
4
Russo JD, Zhang S, Leung JMG, Bogetti AT, Thompson JP, DeGrave AJ, Torrillo PA, Pratt AJ, Wong KF, Xia J, Copperman J, Adelman JL, Zwier MC, LeBard DN, Zuckerman DM, Chong LT. WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications. J Chem Theory Comput 2022;18:638-649. [PMID: 35043623 PMCID: PMC8825686 DOI: 10.1021/acs.jctc.1c01154] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
5
Matsumura Y, Saito S. Microscopic insights into dynamic disorder in the isomerization dynamics of the protein BPTI. J Chem Phys 2021;154:224113. [PMID: 34241205 DOI: 10.1063/5.0055152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
6
Suárez E, Wiewiora RP, Wehmeyer C, Noé F, Chodera JD, Zuckerman DM. What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models. J Chem Theory Comput 2021;17:3119-3133. [PMID: 33904312 PMCID: PMC8127341 DOI: 10.1021/acs.jctc.0c01154] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
7
Bause M, Bereau T. Reweighting non-equilibrium steady-state dynamics along collective variables. J Chem Phys 2021;154:134105. [PMID: 33832234 DOI: 10.1063/5.0042972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
8
Copperman J, Zuckerman DM. Accelerated Estimation of Long-Timescale Kinetics from Weighted Ensemble Simulation via Non-Markovian "Microbin" Analysis. J Chem Theory Comput 2020;16:6763-6775. [PMID: 32990438 PMCID: PMC8045600 DOI: 10.1021/acs.jctc.0c00273] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
9
Sharpe DJ, Wales DJ. Efficient and exact sampling of transition path ensembles on Markovian networks. J Chem Phys 2020;153:024121. [DOI: 10.1063/5.0012128] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
10
Braka A, Garnier N, Bonnet P, Aci-Sèche S. Residence Time Prediction of Type 1 and 2 Kinase Inhibitors from Unbinding Simulations. J Chem Inf Model 2019;60:342-348. [DOI: 10.1021/acs.jcim.9b00497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
11
Agarwal A, Hengartner NW, Gnanakaran S, Voter AF. Computing long time scale biomolecular dynamics using quasi-stationary distribution kinetic Monte Carlo (QSD-KMC). J Chem Phys 2019;151:074109. [PMID: 31438708 DOI: 10.1063/1.5094457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
12
Mostofian B, Zuckerman DM. Statistical Uncertainty Analysis for Small-Sample, High Log-Variance Data: Cautions for Bootstrapping and Bayesian Bootstrapping. J Chem Theory Comput 2019;15:3499-3509. [PMID: 31002504 PMCID: PMC6754704 DOI: 10.1021/acs.jctc.9b00015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
13
Lee HS, Ahn SH, Darve EF. The multi-dimensional generalized Langevin equation for conformational motion of proteins. J Chem Phys 2019;150:174113. [PMID: 31067888 DOI: 10.1063/1.5055573] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
14
Adhikari U, Mostofian B, Copperman J, Subramanian SR, Petersen AA, Zuckerman DM. Computational Estimation of Microsecond to Second Atomistic Folding Times. J Am Chem Soc 2019;141:6519-6526. [PMID: 30892023 PMCID: PMC6660137 DOI: 10.1021/jacs.8b10735] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
15
Saglam AS, Chong LT. Protein-protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations. Chem Sci 2019;10:2360-2372. [PMID: 30881664 PMCID: PMC6385678 DOI: 10.1039/c8sc04811h] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 12/26/2018] [Indexed: 11/21/2022]  Open
16
Xiao J, Salsbury FR. Na+-binding modes involved in thrombin's allosteric response as revealed by molecular dynamics simulations, correlation networks and Markov modeling. Phys Chem Chem Phys 2019;21:4320-4330. [PMID: 30724273 PMCID: PMC6993936 DOI: 10.1039/c8cp07293k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
17
Fujisaki H, Moritsugu K, Mitsutake A, Suetani H. Conformational change of a biomolecule studied by the weighted ensemble method: Use of the diffusion map method to extract reaction coordinates. J Chem Phys 2018;149:134112. [PMID: 30292230 DOI: 10.1063/1.5049420] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
18
Zuckerman DM, Chong LT. Weighted Ensemble Simulation: Review of Methodology, Applications, and Software. Annu Rev Biophys 2017;46:43-57. [PMID: 28301772 PMCID: PMC5896317 DOI: 10.1146/annurev-biophys-070816-033834] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
19
Suárez E, Adelman JL, Zuckerman DM. Accurate Estimation of Protein Folding and Unfolding Times: Beyond Markov State Models. J Chem Theory Comput 2016;12:3473-81. [PMID: 27340835 PMCID: PMC5022777 DOI: 10.1021/acs.jctc.6b00339] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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