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For: Zhou Y, Liu X, Zhang Y, Peng L, Zhang JZH. Residue-specific free energy analysis in ligand bindings to JAK2. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1442596] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Number Cited by Other Article(s)
1
Zheng L, Chen Y, Bao J, He L, Dong S, Qi Y, Zhang JZH. Discovery of novel inhibitors of SARS-CoV-2 main protease. J Biomol Struct Dyn 2022;40:12526-12534. [PMID: 34472424 PMCID: PMC8436407 DOI: 10.1080/07391102.2021.1972041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
2
Liu X, Zheng L, Qin C, Zhang JZH, Sun Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure. J Comput Aided Mol Des 2022;36:735-752. [PMID: 36136209 DOI: 10.1007/s10822-022-00475-0] [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: 07/06/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
3
Pan X, Wang H, Zhang Y, Wang X, Li C, Ji C, Zhang JZH. AA-Score: a New Scoring Function Based on Amino Acid-Specific Interaction for Molecular Docking. J Chem Inf Model 2022;62:2499-2509. [PMID: 35452230 DOI: 10.1021/acs.jcim.1c01537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
4
Zheng L, Yang Y, Bao J, He L, Qi Y, Zhang JZH. Discovery of Novel Inhibitors of CDK2 Using Docking and Physics-based Binding Free Energy Calculation. Chem Biol Drug Des 2022;99:662-673. [PMID: 35148460 DOI: 10.1111/cbdd.14027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 01/04/2022] [Accepted: 01/29/2022] [Indexed: 11/29/2022]
5
Shao G, Bao J, Pan X, He X, Qi Y, Zhang JZH. Analysis of the binding modes of the first- and second-generation antiandrogens with respect to F876L mutation. Chem Biol Drug Des 2021;98:60-72. [PMID: 33905591 DOI: 10.1111/cbdd.13848] [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: 03/03/2021] [Accepted: 04/03/2021] [Indexed: 11/30/2022]
6
Shao G, Bao J, Pan X, He X, Qi Y, Zhang JZH. Computational Analysis of Residue-Specific Binding Free Energies of Androgen Receptor to Ligands. Front Mol Biosci 2021;8:646524. [PMID: 33778009 PMCID: PMC7994597 DOI: 10.3389/fmolb.2021.646524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 01/14/2021] [Indexed: 11/13/2022]  Open
7
Wang Y, Wu S, Wang L, Yang Z, Zhao J, Zhang L. Binding selectivity of inhibitors toward the first over the second bromodomain of BRD4: theoretical insights from free energy calculations and multiple short molecular dynamics simulations. RSC Adv 2020;11:745-759. [PMID: 35423696 PMCID: PMC8693360 DOI: 10.1039/d0ra09469b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 12/17/2020] [Indexed: 12/12/2022]  Open
8
Bao J, He X, Zhang JZ. Development of a New Scoring Function for Virtual Screening: APBScore. J Chem Inf Model 2020;60:6355-6365. [DOI: 10.1021/acs.jcim.0c00474] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
9
Huang D, Tian S, Qi Y, Zhang JZH. Binding Modes of Small-Molecule Inhibitors to the EED Pocket of PRC2. Chemphyschem 2020;21:263-271. [PMID: 31816138 DOI: 10.1002/cphc.201900903] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/30/2019] [Indexed: 12/30/2022]
10
Liu X, Zhao Y, Zhang JZ. Molecular mechanism of ligand bindings to Zika virus at SAM site. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
11
He L, Bao J, Yang Y, Dong S, Zhang L, Qi Y, Zhang JZH. Study of SHMT2 Inhibitors and Their Binding Mechanism by Computational Alanine Scanning. J Chem Inf Model 2019;59:3871-3878. [PMID: 31442042 DOI: 10.1021/acs.jcim.9b00370] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
12
Yang YP, He LP, Bao JX, Qi YF, Zhang JZH. Computational analysis for residue-specific CDK2-inhibitor bindings. CHINESE J CHEM PHYS 2019. [DOI: 10.1063/1674-0068/cjcp1901012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
13
Kohut G, Liwo A, Bősze S, Beke-Somfai T, Samsonov SA. Protein-Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges For Flexible Systems. J Phys Chem B 2018;122:7821-7827. [PMID: 30049211 DOI: 10.1021/acs.jpcb.8b03658] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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