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For: Ngo ST, Nguyen TH, Tung NT, Vu VV, Pham MQ, Mai BK. Characterizing the ligand-binding affinity toward SARS-CoV-2 Mpro via physics- and knowledge-based approaches. Phys Chem Chem Phys 2022;24:29266-29278. [PMID: 36449268 DOI: 10.1039/d2cp04476e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Number Cited by Other Article(s)
1
Wei X, Li M, Tu Y, Wang L. ROC-guided virtual screening, molecular dynamics simulation, and bioactivity validation assessment Z195914464 as a 3CL Mpro inhibitor. Biophys Chem 2025;317:107357. [PMID: 39612624 DOI: 10.1016/j.bpc.2024.107357] [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: 08/28/2024] [Revised: 10/30/2024] [Accepted: 11/20/2024] [Indexed: 12/01/2024]
2
Thai QM, Nguyen TH, Lenon GB, Thu Phung HT, Horng JT, Tran PT, Ngo ST. Estimating AChE inhibitors from MCE database by machine learning and atomistic calculations. J Mol Graph Model 2025;134:108906. [PMID: 39561662 DOI: 10.1016/j.jmgm.2024.108906] [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: 02/02/2024] [Revised: 08/17/2024] [Accepted: 11/06/2024] [Indexed: 11/21/2024]
3
Thai QM, Nguyen TH, Phung HTT, Pham MQ, Pham NKT, Horng JT, Ngo ST. MedChemExpress compounds prevent neuraminidase N1 via physics- and knowledge-based methods. RSC Adv 2024;14:18950-18956. [PMID: 38873542 PMCID: PMC11167619 DOI: 10.1039/d4ra02661f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]  Open
4
Nguyen TH, Thai QM, Pham MQ, Minh PTH, Phung HTT. Machine learning combines atomistic simulations to predict SARS-CoV-2 Mpro inhibitors from natural compounds. Mol Divers 2024;28:553-561. [PMID: 36823394 PMCID: PMC9950021 DOI: 10.1007/s11030-023-10601-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/04/2023] [Indexed: 02/25/2023]
5
Thai QM, Phung HTT, Pham NQA, Horng JT, Tran PT, Tung NT, Ngo ST. Natural compounds inhibit Monkeypox virus methyltransferase VP39 in silico studies. J Biomol Struct Dyn 2024:1-9. [PMID: 38419271 DOI: 10.1080/07391102.2024.2321509] [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: 09/30/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024]
6
Ojha AA, Votapka LW, Amaro RE. QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations. Chem Sci 2023;14:13159-13175. [PMID: 38023523 PMCID: PMC10664576 DOI: 10.1039/d3sc04195f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/22/2023] [Indexed: 12/01/2023]  Open
7
Tam NM, Nguyen TH, Pham MQ, Hong ND, Tung NT, Vu VV, Quang DT, Ngo ST. Upgrading nirmatrelvir to inhibit SARS-CoV-2 Mpro via DeepFrag and free energy calculations. J Mol Graph Model 2023;124:108535. [PMID: 37295158 PMCID: PMC10233213 DOI: 10.1016/j.jmgm.2023.108535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
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