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For: Ding B, Li N, Wang W. Characterizing Binding of Small Molecules. II. Evaluating the Potency of Small Molecules to Combat Resistance Based on Docking Structures. J Chem Inf Model 2013;53:1213-22. [DOI: 10.1021/ci400011c] [Citation(s) in RCA: 18] [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: 01/02/2023]
Number Cited by Other Article(s)
1
Tahir Khan M, Dumont E, Chaudhry AR, Wei DQ. Free energy landscape and thermodynamics properties of novel mutations in PncA of pyrazinamide resistance isolates of Mycobacterium tuberculosis. J Biomol Struct Dyn 2023:1-12. [PMID: 37837425 DOI: 10.1080/07391102.2023.2268216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
2
Wang Q, Wang Z, Tian S, Wang L, Tang R, Yu Y, Ge J, Hou T, Hao H, Sun H. Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning. J Chem Inf Model 2022;62:3993-4007. [PMID: 36040137 DOI: 10.1021/acs.jcim.2c00851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
3
Khan MT, Chinnasamy S, Cui Z, Irfan M, Wei DQ. Mechanistic analysis of A46V, H57Y, and D129N in pyrazinamidase associated with pyrazinamide resistance. Saudi J Biol Sci 2020;27:3150-3156. [PMID: 33100877 PMCID: PMC7569123 DOI: 10.1016/j.sjbs.2020.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 12/20/2022]  Open
4
Ali A, Khan MT, Khan A, Ali S, Chinnasamy S, Akhtar K, Shafiq A, Wei DQ. Pyrazinamide resistance of novel mutations in pncA and their dynamic behavior. RSC Adv 2020;10:35565-35573. [PMID: 35515677 PMCID: PMC9056903 DOI: 10.1039/d0ra06072k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/25/2020] [Indexed: 11/21/2022]  Open
5
Khan MT, Ali S, Zeb MT, Kaushik AC, Malik SI, Wei DQ. Gibbs Free Energy Calculation of Mutation in PncA and RpsA Associated With Pyrazinamide Resistance. Front Mol Biosci 2020;7:52. [PMID: 32328498 PMCID: PMC7160322 DOI: 10.3389/fmolb.2020.00052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/16/2020] [Indexed: 12/16/2022]  Open
6
Wang Z, Sun H, Shen C, Hu X, Gao J, Li D, Cao D, Hou T. Combined strategies in structure-based virtual screening. Phys Chem Chem Phys 2020;22:3149-3159. [PMID: 31995074 DOI: 10.1039/c9cp06303j] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
7
Mehmood A, Khan MT, Kaushik AC, Khan AS, Irfan M, Wei DQ. Structural Dynamics Behind Clinical Mutants of PncA-Asp12Ala, Pro54Leu, and His57Pro of Mycobacterium tuberculosis Associated With Pyrazinamide Resistance. Front Bioeng Biotechnol 2019;7:404. [PMID: 31921809 PMCID: PMC6914729 DOI: 10.3389/fbioe.2019.00404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/26/2019] [Indexed: 11/15/2022]  Open
8
Khan MT, Malik SI. Structural dynamics behind variants in pyrazinamidase and pyrazinamide resistance. J Biomol Struct Dyn 2019;38:3003-3017. [PMID: 31357912 DOI: 10.1080/07391102.2019.1650113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
9
Yang X, Wang Y, Byrne R, Schneider G, Yang S. Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery. Chem Rev 2019;119:10520-10594. [PMID: 31294972 DOI: 10.1021/acs.chemrev.8b00728] [Citation(s) in RCA: 343] [Impact Index Per Article: 68.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
10
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]
11
Khan MT, Khan A, Rehman AU, Wang Y, Akhtar K, Malik SI, Wei DQ. Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance. Sci Rep 2019;9:7482. [PMID: 31097767 PMCID: PMC6522564 DOI: 10.1038/s41598-019-44013-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 04/29/2019] [Indexed: 02/04/2023]  Open
12
Li J, Fu A, Zhang L. An Overview of Scoring Functions Used for Protein-Ligand Interactions in Molecular Docking. Interdiscip Sci 2019;11:320-328. [PMID: 30877639 DOI: 10.1007/s12539-019-00327-w] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 02/06/2019] [Accepted: 03/06/2019] [Indexed: 12/17/2022]
13
Rehman AU, Khan MT, Liu H, Wadood A, Malik SI, Chen HF. Exploring the Pyrazinamide Drug Resistance Mechanism of Clinical Mutants T370P and W403G in Ribosomal Protein S1 of Mycobacterium tuberculosis. J Chem Inf Model 2019;59:1584-1597. [DOI: 10.1021/acs.jcim.8b00956] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
14
Sun H, Pan P, Tian S, Xu L, Kong X, Li Y, Dan Li, Hou T. Constructing and Validating High-Performance MIEC-SVM Models in Virtual Screening for Kinases: A Better Way for Actives Discovery. Sci Rep 2016;6:24817. [PMID: 27102549 PMCID: PMC4840416 DOI: 10.1038/srep24817] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 04/06/2016] [Indexed: 01/23/2023]  Open
15
Li N, Ainsworth RI, Wu M, Ding B, Wang W. MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction. Bioinformatics 2016;32:940-2. [PMID: 26568623 PMCID: PMC4907390 DOI: 10.1093/bioinformatics/btv666] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/13/2015] [Accepted: 11/07/2015] [Indexed: 11/13/2022]  Open
16
Li N, Ainsworth RI, Ding B, Hou T, Wang W. Using Hierarchical Virtual Screening To Combat Drug Resistance of the HIV-1 Protease. J Chem Inf Model 2015;55:1400-12. [DOI: 10.1021/acs.jcim.5b00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
17
Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking: 2012-2013 in review. J Mol Recognit 2015;28:581-604. [PMID: 25808539 DOI: 10.1002/jmr.2471] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Revised: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 12/11/2022]
18
Korkmaz S, Zararsiz G, Goksuluk D. Drug/nondrug classification using Support Vector Machines with various feature selection strategies. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2014;117:51-60. [PMID: 25224081 DOI: 10.1016/j.cmpb.2014.08.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/15/2014] [Accepted: 08/27/2014] [Indexed: 06/03/2023]
19
Heikamp K, Bajorath J. Support vector machines for drug discovery. Expert Opin Drug Discov 2013;9:93-104. [PMID: 24304044 DOI: 10.1517/17460441.2014.866943] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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