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For: 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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Number Cited by Other Article(s)
1
Zhang BW, Fajer M, Chen W, Moraca F, Wang L. Leveraging the Thermodynamics of Protein Conformations in Drug Discovery. J Chem Inf Model 2025;65:252-264. [PMID: 39681511 DOI: 10.1021/acs.jcim.4c01612] [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: 12/18/2024]
2
Pala D, Clark DE. Caught between a ROCK and a hard place: current challenges in structure-based drug design. Drug Discov Today 2024;29:104106. [PMID: 39029868 DOI: 10.1016/j.drudis.2024.104106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/27/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
3
Sun Q, Biswas A, Lyumkis D, Levy R, Deng N. Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization. Viruses 2024;16:76. [PMID: 38257776 PMCID: PMC11154245 DOI: 10.3390/v16010076] [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: 11/25/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024]  Open
4
Sun Q, Biswas A, Lyumkis D, Levy R, Deng N. Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569269. [PMID: 38077045 PMCID: PMC10705364 DOI: 10.1101/2023.11.29.569269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
5
Wang T, Wang L, Zhang X, Shen C, Zhang O, Wang J, Wu J, Jin R, Zhou D, Chen S, Liu L, Wang X, Hsieh CY, Chen G, Pan P, Kang Y, Hou T. Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency. Brief Bioinform 2023;25:bbad486. [PMID: 38171930 PMCID: PMC10764206 DOI: 10.1093/bib/bbad486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024]  Open
6
Geronimo I, De Vivo M. Alchemical Free-Energy Calculations of Watson-Crick and Hoogsteen Base Pairing Interconversion in DNA. J Chem Theory Comput 2022;18:6966-6973. [PMID: 36201305 DOI: 10.1021/acs.jctc.2c00848] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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