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For: Mukhopadhyay A, Tolokh IS, Onufriev AV. Accurate evaluation of charge asymmetry in aqueous solvation. J Phys Chem B 2015;119:6092-100. [PMID: 25830623 DOI: 10.1021/acs.jpcb.5b00602] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Tolokh IS, Folescu DE, Onufriev AV. Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains. J Phys Chem B 2024;128:5855-5873. [PMID: 38860842 PMCID: PMC11194828 DOI: 10.1021/acs.jpcb.4c00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024]
2
Bass L, Elder LH, Folescu DE, Forouzesh N, Tolokh IS, Karpatne A, Onufriev AV. Improving the Accuracy of Physics-Based Hydration-Free Energy Predictions by Machine Learning the Remaining Error Relative to the Experiment. J Chem Theory Comput 2024;20:396-410. [PMID: 38149593 PMCID: PMC10950260 DOI: 10.1021/acs.jctc.3c00981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
3
Wang X, Wang Y, Guo M, Wang X, Li Y, Zhang JZH. Assessment of an Electrostatic Energy-Based Charge Model for Modeling the Electrostatic Interactions in Water Solvent. J Chem Theory Comput 2023;19:6294-6312. [PMID: 37656610 DOI: 10.1021/acs.jctc.3c00467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/03/2023]
4
Zhu J, Xu P, Zhao E, Zhang X, Li X, Li J. The impacts of net charge on the water dispersity of nanoparticles. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
5
Miranda-Quintana RA, Smiatek J. Specific Ion Effects in Different Media: Current Status and Future Challenges. J Phys Chem B 2021;125:13840-13849. [PMID: 34918938 DOI: 10.1021/acs.jpcb.1c07957] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
6
Herbert JM. Dielectric continuum methods for quantum chemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1519] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
7
Onufriev AV, Case DA. Generalized Born Implicit Solvent Models for Biomolecules. Annu Rev Biophys 2019;48:275-296. [PMID: 30857399 PMCID: PMC6645684 DOI: 10.1146/annurev-biophys-052118-115325] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
8
Anandakrishnan R, Izadi S, Onufriev AV. Why Computed Protein Folding Landscapes Are Sensitive to the Water Model. J Chem Theory Comput 2018;15:625-636. [DOI: 10.1021/acs.jctc.8b00485] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
9
Parui S, Jana B. Molecular Insights into the Unusual Structure of an Antifreeze Protein with a Hydrated Core. J Phys Chem B 2018;122:9827-9839. [PMID: 30286600 DOI: 10.1021/acs.jpcb.8b05350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
10
Duignan TT, Baer MD, Mundy CJ. Understanding the scale of the single ion free energy: A critical test of the tetra-phenyl arsonium and tetra-phenyl borate assumption. J Chem Phys 2018;148:222819. [PMID: 29907030 DOI: 10.1063/1.5020171] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
11
Onufriev AV, Izadi S. Water models for biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1347] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
12
Izadi S, Onufriev AV. Accuracy limit of rigid 3-point water models. J Chem Phys 2016;145:074501. [PMID: 27544113 PMCID: PMC4991989 DOI: 10.1063/1.4960175] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/19/2016] [Indexed: 11/14/2022]  Open
13
Reif MM, Hünenberger PH. Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity-Basity Scale Revisited. J Phys Chem B 2016;120:8485-517. [PMID: 27173101 DOI: 10.1021/acs.jpcb.6b02156] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
14
Cumberworth A, Bui JM, Gsponer J. Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models. J Comput Chem 2015;37:629-40. [DOI: 10.1002/jcc.24235] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/25/2015] [Accepted: 10/06/2015] [Indexed: 12/13/2022]
15
Ivanov MV, Talipov MR, Timerghazin QK. Electrostatic point charge fitting as an inverse problem: Revealing the underlying ill-conditioning. J Chem Phys 2015;143:134102. [DOI: 10.1063/1.4932105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
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