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For: Qu S, Huang S, Pan X, Yang L, Mei H. Constructing Interconsistent, Reasonable, and Predictive Models for Both the Kinetic and Thermodynamic Properties of HIV-1 Protease Inhibitors. J Chem Inf Model 2016;56:2061-2068. [PMID: 27624663 DOI: 10.1021/acs.jcim.6b00326] [Citation(s) in RCA: 13] [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: 12/21/2022]
Number Cited by Other Article(s)
1
Xu C, Zhang X, Zhao L, Verkhivker GM, Bai F. Accurate Characterization of Binding Kinetics and Allosteric Mechanisms for the HSP90 Chaperone Inhibitors Using AI-Augmented Integrative Biophysical Studies. JACS AU 2024;4:1632-1645. [PMID: 38665669 PMCID: PMC11040708 DOI: 10.1021/jacsau.4c00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024]
2
Zhou F, Yin S, Xiao Y, Lin Z, Fu W, Zhang YJ. Structure-Kinetic Relationship for Drug Design Revealed by a PLS Model with Retrosynthesis-Based Pre-Trained Molecular Representation and Molecular Dynamics Simulation. ACS OMEGA 2023;8:18312-18322. [PMID: 37251166 PMCID: PMC10210189 DOI: 10.1021/acsomega.3c02294] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
3
Liu H, Su M, Lin HX, Wang R, Li Y. Public Data Set of Protein-Ligand Dissociation Kinetic Constants for Quantitative Structure-Kinetics Relationship Studies. ACS OMEGA 2022;7:18985-18996. [PMID: 35694511 PMCID: PMC9178723 DOI: 10.1021/acsomega.2c02156] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/13/2022] [Indexed: 06/01/2023]
4
Penna E, Niso M, Podlewska S, Volpicelli F, Crispino M, Perrone-Capano C, Bojarski AJ, Lacivita E, Leopoldo M. In Vitro and In Silico Analysis of the Residence Time of Serotonin 5-HT7 Receptor Ligands with Arylpiperazine Structure: A Structure-Kinetics Relationship Study. ACS Chem Neurosci 2022;13:497-509. [PMID: 35099177 DOI: 10.1021/acschemneuro.1c00710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
5
Ritonavir and xk263 Binding-Unbinding with HIV-1 Protease: Pathways, Energy and Comparison. LIFE (BASEL, SWITZERLAND) 2022;12:life12010116. [PMID: 35054509 PMCID: PMC8779838 DOI: 10.3390/life12010116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 01/22/2023]
6
Potterton A, Heifetz A, Townsend-Nicholson A. Predicting Residence Time of GPCR Ligands with Machine Learning. Methods Mol Biol 2022;2390:191-205. [PMID: 34731470 DOI: 10.1007/978-1-0716-1787-8_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
7
Nunes-Alves A, Ormersbach F, Wade RC. Prediction of the Drug-Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis. J Chem Inf Model 2021;61:3708-3721. [PMID: 34197096 DOI: 10.1021/acs.jcim.1c00639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
8
Amangeldiuly N, Karlov D, Fedorov MV. Baseline Model for Predicting Protein–Ligand Unbinding Kinetics through Machine Learning. J Chem Inf Model 2020;60:5946-5956. [DOI: 10.1021/acs.jcim.0c00450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
9
Huang S, Chen L, Mei H, Zhang D, Shi T, Kuang Z, Heng Y, Xu L, Pan X. In Silico Prediction of the Dissociation Rate Constants of Small Chemical Ligands by 3D-Grid-Based VolSurf Method. Int J Mol Sci 2020;21:ijms21072456. [PMID: 32252223 PMCID: PMC7177943 DOI: 10.3390/ijms21072456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/30/2020] [Indexed: 12/26/2022]  Open
10
Kokh DB, Kaufmann T, Kister B, Wade RC. Machine Learning Analysis of τRAMD Trajectories to Decipher Molecular Determinants of Drug-Target Residence Times. Front Mol Biosci 2019;6:36. [PMID: 31179286 PMCID: PMC6543870 DOI: 10.3389/fmolb.2019.00036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/02/2019] [Indexed: 12/25/2022]  Open
11
Huang S, Zhang D, Mei H, Kevin M, Qu S, Pan X, Lu L. SMD-Based Interaction-Energy Fingerprints Can Predict Accurately the Dissociation Rate Constants of HIV-1 Protease Inhibitors. J Chem Inf Model 2018;59:159-169. [DOI: 10.1021/acs.jcim.8b00567] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
12
Huang S, Mei H, Zhang D, Ren Y, Kevin M, Pan X. The emerging chemical patterns applied in predicting human toll-like receptor 8 agonists. MEDCHEMCOMM 2018;9:1961-1971. [PMID: 30568763 PMCID: PMC6256730 DOI: 10.1039/c8md00276b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
13
De Benedetti PG, Fanelli F. Computational modeling approaches to quantitative structure-binding kinetics relationships in drug discovery. Drug Discov Today 2018;23:1396-1406. [PMID: 29574212 DOI: 10.1016/j.drudis.2018.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 02/22/2018] [Accepted: 03/19/2018] [Indexed: 11/22/2022]
14
Ramamurthy M, Sankar S, Kannangai R, Nandagopal B, Sridharan G. Application of viromics: a new approach to the understanding of viral infections in humans. Virusdisease 2017;28:349-359. [PMID: 29291225 DOI: 10.1007/s13337-017-0415-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/17/2017] [Indexed: 12/19/2022]  Open
15
Bruce NJ, Ganotra GK, Kokh DB, Sadiq SK, Wade RC. New approaches for computing ligand-receptor binding kinetics. Curr Opin Struct Biol 2017;49:1-10. [PMID: 29132080 DOI: 10.1016/j.sbi.2017.10.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/22/2017] [Accepted: 10/01/2017] [Indexed: 02/08/2023]
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