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For: Forouzesh N, Izadi S, Onufriev AV. Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies. J Chem Inf Model 2017;57:2505-2513. [DOI: 10.1021/acs.jcim.7b00192] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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
Risheh A, Rebel A, Nerenberg PS, Forouzesh N. Calculation of protein-ligand binding entropies using a rule-based molecular fingerprint. Biophys J 2024:S0006-3495(24)00182-6. [PMID: 38481102 DOI: 10.1016/j.bpj.2024.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/21/2023] [Accepted: 03/08/2024] [Indexed: 03/28/2024]  Open
3
Chen J, Xu Y, Yang X, Cang Z, Geng W, Wei GW. Poisson-Boltzmann-based machine learning model for electrostatic analysis. Biophys J 2024:S0006-3495(24)00107-3. [PMID: 38356263 DOI: 10.1016/j.bpj.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]  Open
4
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]
5
Case D, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, Lee TS, Li P, Liu J, Luchko T, Luo R, Manathunga M, Machado MR, Nguyen HM, O’Hearn KA, Onufriev AV, Pan F, Pantano S, Qi R, Rahnamoun A, Risheh A, Schott-Verdugo S, Shajan A, Swails J, Wang J, Wei H, Wu X, Wu Y, Zhang S, Zhao S, Zhu Q, Cheatham TE, Roe DR, Roitberg A, Simmerling C, York DM, Nagan MC, Merz KM. AmberTools. J Chem Inf Model 2023;63:6183-6191. [PMID: 37805934 PMCID: PMC10598796 DOI: 10.1021/acs.jcim.3c01153] [Citation(s) in RCA: 92] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/10/2023]
6
Sagar D, Risheh A, Sheikh N, Forouzesh N. Physics-Guided Deep Generative Model for New Ligand Discovery. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2023;2023:10.1145/3584371.3613067. [PMID: 38706556 PMCID: PMC11067829 DOI: 10.1145/3584371.3613067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
7
Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022;122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
8
Cain S, Risheh A, Forouzesh N. A Physics-Guided Neural Network for Predicting Protein–Ligand Binding Free Energy: From Host–Guest Systems to the PDBbind Database. Biomolecules 2022;12:biom12070919. [PMID: 35883475 PMCID: PMC9312865 DOI: 10.3390/biom12070919] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 11/16/2022]  Open
9
Chen J, Geng W, Wei GW. MLIMC: Machine Learning-Based Implicit-Solvent Monte Carlo. CHINESE J CHEM PHYS 2021;34:683-694. [PMID: 35024043 PMCID: PMC8752096 DOI: 10.1063/1674-0068/cjcp2109150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
10
Wang E, Fu W, Jiang D, Sun H, Wang J, Zhang X, Weng G, Liu H, Tao P, Hou T. VAD-MM/GBSA: A Variable Atomic Dielectric MM/GBSA Model for Improved Accuracy in Protein-Ligand Binding Free Energy Calculations. J Chem Inf Model 2021;61:2844-2856. [PMID: 34014672 DOI: 10.1021/acs.jcim.1c00091] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
11
Forouzesh N, Mishra N. An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor. Molecules 2021;26:2383. [PMID: 33923909 PMCID: PMC8074138 DOI: 10.3390/molecules26082383] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 12/23/2022]  Open
12
Forouzesh N, Onufriev AV. MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.25.267625. [PMID: 32869029 PMCID: PMC7457614 DOI: 10.1101/2020.08.25.267625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
13
Forouzesh N, Mukhopadhyay A, Watson LT, Onufriev AV. Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding. J Chem Theory Comput 2020;16:4669-4684. [PMID: 32450041 PMCID: PMC8594251 DOI: 10.1021/acs.jctc.0c00142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
14
Horvath D, Marcou G, Varnek A. "Big Data" Fast Chemoinformatics Model to Predict Generalized Born Radius and Solvent Accessibility as a Function of Geometry. J Chem Inf Model 2020;60:2951-2965. [PMID: 32374171 DOI: 10.1021/acs.jcim.9b01172] [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]
15
Wang E, Liu H, Wang J, Weng G, Sun H, Wang Z, Kang Y, Hou T. Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein–Ligand Binding Affinities. J Chem Inf Model 2020;60:5353-5365. [DOI: 10.1021/acs.jcim.0c00024] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
16
Wang E, Weng G, Sun H, Du H, Zhu F, Chen F, Wang Z, Hou T. Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein-protein Interactions. Phys Chem Chem Phys 2019;21:18958-18969. [PMID: 31453590 DOI: 10.1039/c9cp04096j] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
17
Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019;119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
18
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]
19
Tolokh IS, Thomas DG, Onufriev AV. Explicit ions/implicit water generalized Born model for nucleic acids. J Chem Phys 2018;148:195101. [PMID: 30307229 DOI: 10.1063/1.5027260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
20
Huang Y, Harris RC, Shen J. Generalized Born Based Continuous Constant pH Molecular Dynamics in Amber: Implementation, Benchmarking and Analysis. J Chem Inf Model 2018;58:1372-1383. [PMID: 29949356 DOI: 10.1021/acs.jcim.8b00227] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
21
Izadi S, Harris RC, Fenley MO, Onufriev AV. Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies. J Chem Theory Comput 2018;14:1656-1670. [PMID: 29378399 DOI: 10.1021/acs.jctc.7b00886] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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