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For: Corrigan RA, Qi G, Thiel AC, Lynn JR, Walker BD, Casavant TL, Lagardere L, Piquemal JP, Ponder JW, Ren P, Schnieders MJ. Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field. J Chem Theory Comput 2021;17:2323-2341. [PMID: 33769814 DOI: 10.1021/acs.jctc.0c01286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Number Cited by Other Article(s)
1
Wang X, Liu H, Li Y, Li J, Li WL. TinkerModeller: An Efficient Tool for Building Biological Systems in Tinker Simulations. J Chem Theory Comput 2025;21:2712-2722. [PMID: 39999350 PMCID: PMC11912192 DOI: 10.1021/acs.jctc.4c01463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2024] [Revised: 02/19/2025] [Accepted: 02/20/2025] [Indexed: 02/27/2025]
2
Yu JW, Kim S, Ryu JH, Lee WB, Yoon TJ. Spatiotemporal characterization of water diffusion anomalies in saline solutions using machine learning force field. SCIENCE ADVANCES 2024;10:eadp9662. [PMID: 39661667 PMCID: PMC11633738 DOI: 10.1126/sciadv.adp9662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 11/04/2024] [Indexed: 12/13/2024]
3
Teng X, Yu W, MacKerell AD. Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ. J Chem Theory Comput 2024;20:10034-10044. [PMID: 39536452 PMCID: PMC11598640 DOI: 10.1021/acs.jctc.4c00966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
4
Gogal RA, Nessler AJ, Thiel AC, Bernabe HV, Corrigan Grove RA, Cousineau LM, Litman JM, Miller JM, Qi G, Speranza MJ, Tollefson MR, Fenn TD, Michaelson JJ, Okada O, Piquemal JP, Ponder JW, Shen J, Smith RJH, Yang W, Ren P, Schnieders MJ. Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment. J Chem Phys 2024;161:012501. [PMID: 38958156 PMCID: PMC11223778 DOI: 10.1063/5.0214652] [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: 04/18/2024] [Accepted: 06/17/2024] [Indexed: 07/04/2024]  Open
5
Wang Y, Liu L, Gao Y, Zhao J, Liu C, Gong L, Yang Z. Development of a QM/MM(ABEEM) method for the deprotonation of neutral and cation radicals in the G-tetrad and GGX(8-oxo-G) tetrad. Phys Chem Chem Phys 2023;26:504-516. [PMID: 38084041 DOI: 10.1039/d3cp04357f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
6
Corrigan RA, Thiel AC, Lynn JR, Casavant TL, Ren P, Ponder JW, Schnieders MJ. A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model. J Chem Phys 2023;159:054102. [PMID: 37526158 PMCID: PMC10396400 DOI: 10.1063/5.0158914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]  Open
7
The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides. Int J Mol Sci 2022;23:ijms232113514. [PMID: 36362296 PMCID: PMC9654426 DOI: 10.3390/ijms232113514] [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: 10/14/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]  Open
8
Wang KW, Lee J, Zhang H, Suh D, Im W. CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs. J Phys Chem B 2022;126:7354-7364. [PMID: 36117287 DOI: 10.1021/acs.jpcb.2c05294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
9
Walker B, Liu C, Wait E, Ren P. Automation of AMOEBA polarizable force field for small molecules: Poltype 2. J Comput Chem 2022;43:1530-1542. [PMID: 35778723 PMCID: PMC9329217 DOI: 10.1002/jcc.26954] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/02/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022]
10
He X, Walker B, Man VH, Ren P, Wang J. Recent progress in general force fields of small molecules. Curr Opin Struct Biol 2022;72:187-193. [PMID: 34942567 PMCID: PMC8860847 DOI: 10.1016/j.sbi.2021.11.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 09/10/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023]
11
Wu R, Matta M, Paulsen BD, Rivnay J. Operando Characterization of Organic Mixed Ionic/Electronic Conducting Materials. Chem Rev 2022;122:4493-4551. [PMID: 35026108 DOI: 10.1021/acs.chemrev.1c00597] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
12
Michael E, Simonson T. How much can physics do for protein design? Curr Opin Struct Biol 2021;72:46-54. [PMID: 34461593 DOI: 10.1016/j.sbi.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 01/03/2023]
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