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For: Zhang BW, Deng N, Tan Z, Levy RM. Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which Are Far from Equilibrium. J Chem Theory Comput 2017;13:4660-4674. [PMID: 28902500 PMCID: PMC5897113 DOI: 10.1021/acs.jctc.7b00651] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
Suruzhon M, Abdel-Maksoud K, Bodnarchuk MS, Ciancetta A, Wall ID, Essex JW. Enhancing torsional sampling using fully adaptive simulated tempering. J Chem Phys 2024;160:154110. [PMID: 38639317 DOI: 10.1063/5.0190659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/23/2024] [Indexed: 04/20/2024]  Open
2
Brooks CL, MacKerell AD, Post CB, Nilsson L. Biomolecular dynamics in the 21st century. Biochim Biophys Acta Gen Subj 2024;1868:130534. [PMID: 38065235 PMCID: PMC10842176 DOI: 10.1016/j.bbagen.2023.130534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
3
Galama MM, Wu H, Krämer A, Sadeghi M, Noé F. Stochastic Approximation to MBAR and TRAM: Batchwise Free Energy Estimation. J Chem Theory Comput 2023;19:758-766. [PMID: 36689637 DOI: 10.1021/acs.jctc.2c00976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
4
Hong Y, Najafi S, Casey T, Shea JE, Han SI, Hwang DS. Hydrophobicity of arginine leads to reentrant liquid-liquid phase separation behaviors of arginine-rich proteins. Nat Commun 2022;13:7326. [PMID: 36443315 PMCID: PMC9705477 DOI: 10.1038/s41467-022-35001-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022]  Open
5
Vymětal J, Vondrášek J. Iterative Landmark-Based Umbrella Sampling (ILBUS) Protocol for Sampling of Conformational Space of Biomolecules. J Chem Inf Model 2022;62:4783-4798. [PMID: 36122323 DOI: 10.1021/acs.jcim.2c00370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
6
Arasteh S, Zhang BW, Levy RM. Protein Loop Conformational Free Energy Changes via an Alchemical Path without Reaction Coordinates. J Phys Chem Lett 2021;12:4368-4377. [PMID: 33938761 PMCID: PMC8170697 DOI: 10.1021/acs.jpclett.1c00778] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
7
Hahn DF, Zarotiadis RA, Hünenberger PH. The Conveyor Belt Umbrella Sampling (CBUS) Scheme: Principle and Application to the Calculation of the Absolute Binding Free Energies of Alkali Cations to Crown Ethers. J Chem Theory Comput 2020;16:2474-2493. [DOI: 10.1021/acs.jctc.9b00998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
8
Hahn DF, Hünenberger PH. Alchemical Free-Energy Calculations by Multiple-Replica λ-Dynamics: The Conveyor Belt Thermodynamic Integration Scheme. J Chem Theory Comput 2019;15:2392-2419. [PMID: 30821973 DOI: 10.1021/acs.jctc.8b00782] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
9
Zhang BW, Arasteh S, Levy RM. The UWHAM and SWHAM Software Package. Sci Rep 2019;9:2803. [PMID: 30808938 PMCID: PMC6391495 DOI: 10.1038/s41598-019-39420-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/21/2019] [Indexed: 11/09/2022]  Open
10
Zhang BW, Cui D, Matubayasi N, Levy RM. The Excess Chemical Potential of Water at the Interface with a Protein from End Point Simulations. J Phys Chem B 2018;122:4700-4707. [PMID: 29634902 DOI: 10.1021/acs.jpcb.8b02666] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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