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For: Levintov L, Paul S, Vashisth H. Reaction Coordinate and Thermodynamics of Base Flipping in RNA. J Chem Theory Comput 2021;17:1914-1921. [PMID: 33594886 DOI: 10.1021/acs.jctc.0c01199] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Number Cited by Other Article(s)
1
Wright ZM, Butay KJ, Krahn JM, Wilson IM, Gabel SA, DeRose EF, Hissein IS, Williams JG, Borgnia MJ, Frazier MN, Mueller GA, Stanley RE. Spontaneous base flipping helps drive Nsp15's preferences in double stranded RNA substrates. Nat Commun 2025;16:391. [PMID: 39755678 DOI: 10.1038/s41467-024-55682-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 12/20/2024] [Indexed: 01/06/2025]  Open
2
Levintov L, Vashisth H. Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop. J Phys Chem B 2024;128:3157-3166. [PMID: 38535997 PMCID: PMC11000223 DOI: 10.1021/acs.jpcb.4c00522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/10/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
3
Sato R, Suzuki K, Yasuda Y, Suenaga A, Fukui K. RNAapt3D: RNA aptamer 3D-structural modeling database. Biophys J 2022;121:4770-4776. [PMID: 36146935 PMCID: PMC9808543 DOI: 10.1016/j.bpj.2022.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/17/2022] [Accepted: 09/20/2022] [Indexed: 01/07/2023]  Open
4
Schwartz SD. Perspective: Path Sampling Methods Applied to Enzymatic Catalysis. J Chem Theory Comput 2022;18:6397-6406. [PMID: 36305863 PMCID: PMC9677451 DOI: 10.1021/acs.jctc.2c00734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
5
Wang SD, Zhang RB, Eriksson LA. Markov state models elucidate the stability of DNA influenced by the chiral 5S-Tg base. Nucleic Acids Res 2022;50:9072-9082. [PMID: 35979954 PMCID: PMC9458442 DOI: 10.1093/nar/gkac691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/15/2022] [Accepted: 07/30/2022] [Indexed: 12/24/2022]  Open
6
Copeland M, Do HN, Votapka L, Joshi K, Wang J, Amaro RE, Miao Y. Gaussian Accelerated Molecular Dynamics in OpenMM. J Phys Chem B 2022;126:5810-5820. [PMID: 35895977 PMCID: PMC9773147 DOI: 10.1021/acs.jpcb.2c03765] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
7
Kikutsuji T, Mori Y, Okazaki KI, Mori T, Kim K, Matubayasi N. Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI). J Chem Phys 2022;156:154108. [DOI: 10.1063/5.0087310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
8
Paul TK, Taraphder S. Nonlinear Reaction Coordinate of an Enzyme Catalyzed Proton Transfer Reaction. J Phys Chem B 2022;126:1413-1425. [PMID: 35138854 DOI: 10.1021/acs.jpcb.1c08760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
9
Wang SD, Eriksson LA, Zhang RB. Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond. J Chem Inf Model 2022;62:386-398. [PMID: 34994562 PMCID: PMC8790752 DOI: 10.1021/acs.jcim.1c01169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
10
Patel SJ, Van Lehn RC. Analysis of Charged Peptide Loop-Flipping across a Lipid Bilayer Using the String Method with Swarms of Trajectories. J Phys Chem B 2021;125:5862-5873. [PMID: 34033491 DOI: 10.1021/acs.jpcb.1c02810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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