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For: Wan S, Bhati AP, Wright DW, Wall ID, Graves AP, Green D, Coveney PV. Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors. J Chem Inf Model 2022;62:2561-2570. [PMID: 35508076 PMCID: PMC9131449 DOI: 10.1021/acs.jcim.2c00255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Number Cited by Other Article(s)
1
Pushkaran AC, Arabi AA. Accurate prediction of DNA-Intercalator binding energies: Ensemble of short or long molecular dynamics simulations? Int J Biol Macromol 2025;306:141408. [PMID: 39993670 DOI: 10.1016/j.ijbiomac.2025.141408] [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: 12/11/2024] [Revised: 01/29/2025] [Accepted: 02/21/2025] [Indexed: 02/26/2025]
2
Yue Y, Cheng Y, Marquet C, Xiao C, Guo J, Li S, He S. Meta-Learning Enables Complex Cluster-Specific Few-Shot Binding Affinity Prediction for Protein-Protein Interactions. J Chem Inf Model 2025;65:580-588. [PMID: 39772708 DOI: 10.1021/acs.jcim.4c01607] [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: 01/11/2025]
3
Bhati A, Wan S, Coveney PV. Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations. J Chem Theory Comput 2025;21:440-462. [PMID: 39680850 PMCID: PMC11736689 DOI: 10.1021/acs.jctc.4c01389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 11/28/2024] [Accepted: 12/02/2024] [Indexed: 12/18/2024]
4
Yue Y, Li S, Cheng Y, Wang L, Hou T, Zhu Z, He S. Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction. Nat Commun 2024;15:9629. [PMID: 39511202 PMCID: PMC11544137 DOI: 10.1038/s41467-024-53583-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 10/16/2024] [Indexed: 11/15/2024]  Open
5
Loeffler HH, Wan S, Klähn M, Bhati AP, Coveney PV. Optimal Molecular Design: Generative Active Learning Combining REINVENT with Precise Binding Free Energy Ranking Simulations. J Chem Theory Comput 2024;20. [PMID: 39225482 PMCID: PMC11428133 DOI: 10.1021/acs.jctc.4c00576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 08/08/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
6
Wan S, Bhati AP, Wade AD, Coveney PV. Ensemble-Based Approaches Ensure Reliability and Reproducibility. J Chem Inf Model 2023;63:6959-6963. [PMID: 37965695 PMCID: PMC10685440 DOI: 10.1021/acs.jcim.3c01654] [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: 10/13/2023] [Indexed: 11/16/2023]
7
Wan S, Bhati AP, Coveney PV. Comparison of Equilibrium and Nonequilibrium Approaches for Relative Binding Free Energy Predictions. J Chem Theory Comput 2023;19:7846-7860. [PMID: 37862058 PMCID: PMC10653111 DOI: 10.1021/acs.jctc.3c00842] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Indexed: 10/21/2023]
8
The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase. Sci Rep 2022;12:10433. [PMID: 35729177 PMCID: PMC9211793 DOI: 10.1038/s41598-022-13319-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/23/2022] [Indexed: 11/08/2022]  Open
9
Wade A, Bhati AP, Wan S, Coveney PV. Alchemical Free Energy Estimators and Molecular Dynamics Engines: Accuracy, Precision, and Reproducibility. J Chem Theory Comput 2022;18:3972-3987. [PMID: 35609233 PMCID: PMC9202356 DOI: 10.1021/acs.jctc.2c00114] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Indexed: 11/28/2022]
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