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Number Cited by Other Article(s)
1
Sun Y, Jia C, Zhang S, Zhang Q, Chen J, Liu X. Accelerated molecular dynamics study of the interaction mechanism between small molecule inhibitors and phosphoglycerate mutase 1. Phys Chem Chem Phys 2024;26:26784-26798. [PMID: 39403732 DOI: 10.1039/d4cp03309d] [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: 11/01/2024]
2
Chen J, Wang J, Yang W, Zhao L, Hu G. Conformations of KRAS4B Affected by Its Partner Binding and G12C Mutation: Insights from GaMD Trajectory-Image Transformation-Based Deep Learning. J Chem Inf Model 2024;64:6880-6898. [PMID: 39197061 DOI: 10.1021/acs.jcim.4c01174] [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: 08/30/2024]
3
Wang B, Wang J, Yang W, Zhao L, Wei B, Chen J. Unveiling Allosteric Regulation and Binding Mechanism of BRD9 through Molecular Dynamics Simulations and Markov Modeling. Molecules 2024;29:3496. [PMID: 39124901 PMCID: PMC11314499 DOI: 10.3390/molecules29153496] [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: 06/25/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]  Open
4
Zhao L, Wang J, Yang W, Zhao K, Sun Q, Chen J. Unveiling Conformational States of CDK6 Caused by Binding of Vcyclin Protein and Inhibitor by Combining Gaussian Accelerated Molecular Dynamics and Deep Learning. Molecules 2024;29:2681. [PMID: 38893554 PMCID: PMC11174096 DOI: 10.3390/molecules29112681] [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: 05/08/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024]  Open
5
Chen J, Wang J, Yang W, Zhao L, Zhao J, Hu G. Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning. Molecules 2024;29:2317. [PMID: 38792177 PMCID: PMC11123822 DOI: 10.3390/molecules29102317] [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: 04/23/2024] [Revised: 05/09/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024]  Open
6
Wang J, Yang W, Zhao L, Wei B, Chen J. Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning. Molecules 2024;29:1857. [PMID: 38675678 PMCID: PMC11054187 DOI: 10.3390/molecules29081857] [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: 04/03/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024]  Open
7
Bao H, Wang W, Sun H, Chen J. The switch states of the GDP-bound HRAS affected by point mutations: a study from Gaussian accelerated molecular dynamics simulations and free energy landscapes. J Biomol Struct Dyn 2024;42:3363-3381. [PMID: 37216340 DOI: 10.1080/07391102.2023.2213355] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
8
Shen C, Yin J, Wang M, Yu Z, Xu X, Zhou Z, Hu Y, Xia C, Hu G. Mutations influence the conformational dynamics of the GDP/KRAS complex. J Biomol Struct Dyn 2024:1-14. [PMID: 38529923 DOI: 10.1080/07391102.2024.2331627] [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: 01/22/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
9
Yu Z, Wang Z, Cui X, Cao Z, Zhang W, Sun K, Hu G. Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics. Molecules 2024;29:645. [PMID: 38338389 PMCID: PMC10856033 DOI: 10.3390/molecules29030645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/01/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]  Open
10
Jia K, Li C, Xu M, Dai G, Zhou J, Chen B, Zou J, Li J, Zhang Q, Ju W. Exploring the mechanism of Si-Ni-San against depression by UPLC-Q-TOF-MS/MS integrated with network pharmacology: experimental research. Ann Med Surg (Lond) 2024;86:172-189. [PMID: 38222693 PMCID: PMC10783272 DOI: 10.1097/ms9.0000000000001464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/21/2023] [Indexed: 01/16/2024]  Open
11
Chen J, Wang W, Sun H, He W. Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters. Mini Rev Med Chem 2024;24:1323-1333. [PMID: 38265367 DOI: 10.2174/0113895575252165231122095555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 01/25/2024]
12
Xu B, Chen Y, Xue W. Computational Protein Design - Where it goes? Curr Med Chem 2024;31:2841-2854. [PMID: 37272467 DOI: 10.2174/0929867330666230602143700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/18/2023] [Accepted: 03/15/2023] [Indexed: 06/06/2023]
13
Abedi Dorcheh F, Balmeh N, Hejazi SH, Allahyari Fard N. Investigation of the mutated antimicrobial peptides to inhibit ACE2, TMPRSS2 and GRP78 receptors of SARS-CoV-2 and angiotensin II type 1 receptor (AT1R) as well as controlling COVID-19 disease. J Biomol Struct Dyn 2023:1-24. [PMID: 38109185 DOI: 10.1080/07391102.2023.2292307] [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: 12/08/2022] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
14
Eltaib L, Alzain AA. Targeting the omicron variant of SARS-CoV-2 with phytochemicals from Saudi medicinal plants: molecular docking combined with molecular dynamics investigations. J Biomol Struct Dyn 2023;41:9732-9744. [PMID: 36369836 DOI: 10.1080/07391102.2022.2146203] [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: 09/14/2022] [Accepted: 11/05/2022] [Indexed: 11/14/2022]
15
Fu T, Zeng S, Zheng Q, Zhu F. The Important Role of Transporter Structures in Drug Disposition, Efficacy, and Toxicity. Drug Metab Dispos 2023;51:1316-1323. [PMID: 37295948 DOI: 10.1124/dmd.123.001275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/27/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]  Open
16
Hu G, Zhang Y, Yu Z, Cui T, Cui W. Dynamical characterization and multiple unbinding paths of two PreQ1 ligands in one pocket. Phys Chem Chem Phys 2023;25:24004-24015. [PMID: 37646322 DOI: 10.1039/d3cp03142j] [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: 09/01/2023]
17
Delre P, Contino M, Alberga D, Saviano M, Corriero N, Mangiatordi GF. ALPACA: A machine Learning Platform for Affinity and selectivity profiling of CAnnabinoids receptors modulators. Comput Biol Med 2023;164:107314. [PMID: 37572442 DOI: 10.1016/j.compbiomed.2023.107314] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/10/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
18
Deng S, Zhang H, Gou R, Luo D, Liu Z, Zhu F, Xue W. Structure-Based Discovery of a Novel Allosteric Inhibitor against Human Dopamine Transporter. J Chem Inf Model 2023. [PMID: 37410882 DOI: 10.1021/acs.jcim.3c00477] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
19
Yang F, Wang Y, Yan D, Liu Z, Wei B, Chen J, He W. Binding Mechanism of Inhibitors to Heat Shock Protein 90 Investigated by Multiple Independent Molecular Dynamics Simulations and Prediction of Binding Free Energy. Molecules 2023;28:4792. [PMID: 37375347 DOI: 10.3390/molecules28124792] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]  Open
20
Wang Y, Yang F, Yan D, Zeng Y, Wei B, Chen J, He W. Identification Mechanism of BACE1 on Inhibitors Probed by Using Multiple Separate Molecular Dynamics Simulations and Comparative Calculations of Binding Free Energies. Molecules 2023;28:4773. [PMID: 37375328 DOI: 10.3390/molecules28124773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]  Open
21
Gosu V, Sasidharan S, Saudagar P, Radhakrishnan K, Lee HK, Shin D. Deciphering the intrinsic dynamics of unphosphorylated IRAK4 kinase bound to type I and type II inhibitors. Comput Biol Med 2023;160:106978. [DOI: https:/doi.org/10.1016/j.compbiomed.2023.106978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2023]
22
Hossain A, Rahman ME, Rahman MS, Nasirujjaman K, Matin MN, Faruqe MO, Rabbee MF. Identification of medicinal plant-based phytochemicals as a potential inhibitor for SARS-CoV-2 main protease (Mpro) using molecular docking and deep learning methods. Comput Biol Med 2023;157:106785. [PMID: 36931201 PMCID: PMC10008098 DOI: 10.1016/j.compbiomed.2023.106785] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/15/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023]
23
Gul K, Zaman N, Azam SS. Roxadustat and its failure: A comparative dynamic study. J Mol Graph Model 2023;120:108422. [PMID: 36708643 DOI: 10.1016/j.jmgm.2023.108422] [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: 11/24/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
24
Gosu V, Sasidharan S, Saudagar P, Radhakrishnan K, Lee HK, Shin D. Deciphering the intrinsic dynamics of unphosphorylated IRAK4 kinase bound to type I and type II inhibitors. Comput Biol Med 2023;160:106978. [PMID: 37172355 DOI: 10.1016/j.compbiomed.2023.106978] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/14/2023]
25
Tu G, Xu B, Luo D, Liu J, Liu Z, Chen G, Xue W. Multi-state Model-Based Identification of Cryptic Allosteric Sites on Human Serotonin Transporter. ACS Chem Neurosci 2023;14:1686-1694. [PMID: 37067527 DOI: 10.1021/acschemneuro.3c00155] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]  Open
26
Shi S, Zheng L, Ren Y, Wang Z. Impacts of Mutations in the P-Loop on Conformational Alterations of KRAS Investigated with Gaussian Accelerated Molecular Dynamics Simulations. Molecules 2023;28:molecules28072886. [PMID: 37049650 PMCID: PMC10095679 DOI: 10.3390/molecules28072886] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 04/14/2023]  Open
27
Kumari S, Kumar P. Design and Computational Analysis of an MMP9 Inhibitor in Hypoxia-Induced Glioblastoma Multiforme. ACS OMEGA 2023;8:10565-10590. [PMID: 36969457 PMCID: PMC10035023 DOI: 10.1021/acsomega.3c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
28
Babaoglu ZY, Kilic D. Virtual screening, molecular simulations and bioassays: Discovering novel microsomal prostaglandin E Synthase-1 (mPGES-1) inhibitors. Comput Biol Med 2023;155:106616. [PMID: 36780799 DOI: 10.1016/j.compbiomed.2023.106616] [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: 06/14/2022] [Revised: 01/05/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
29
Yan TC, Yue ZX, Xu HQ, Liu YH, Hong YF, Chen GX, Tao L, Xie T. A systematic review of state-of-the-art strategies for machine learning-based protein function prediction. Comput Biol Med 2023;154:106446. [PMID: 36680931 DOI: 10.1016/j.compbiomed.2022.106446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
30
Bao HY, Wang W, Sun HB, Chen JZ. Binding modes of GDP, GTP and GNP to NRAS deciphered by using Gaussian accelerated molecular dynamics simulations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023;34:65-89. [PMID: 36762439 DOI: 10.1080/1062936x.2023.2165542] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/31/2022] [Indexed: 06/18/2023]
31
Chen J, Zeng Q, Wang W, Sun H, Hu G. Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations. J Chem Inf Model 2022;62:6118-6132. [PMID: 36440874 DOI: 10.1021/acs.jcim.2c00961] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
32
Liu J, Sun T, Liu S, Liu J, Fang S, Tan S, Zeng Y, Zhang B, Li W. Dissecting the molecular mechanism of cepharanthine against COVID-19, based on a network pharmacology strategy combined with RNA-sequencing analysis, molecular docking, and molecular dynamics simulation. Comput Biol Med 2022;151:106298. [PMID: 36403355 PMCID: PMC9671524 DOI: 10.1016/j.compbiomed.2022.106298] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/10/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
33
Hajji H, Alaqarbeh M, Lakhlifi T, Ajana MA, Alsakhen N, Bouachrine M. Computational approach investigation bioactive molecules from Saussurea Costus plant as SARS-CoV-2 main protease inhibitors using reverse docking, molecular dynamics simulation, and pharmacokinetic ADMET parameters. Comput Biol Med 2022;150:106209. [PMID: 36257276 PMCID: PMC9554895 DOI: 10.1016/j.compbiomed.2022.106209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 09/23/2022] [Accepted: 10/09/2022] [Indexed: 11/17/2022]
34
Liao J, Chen H, Wei L, Wei L. GSAML-DTA: An interpretable drug-target binding affinity prediction model based on graph neural networks with self-attention mechanism and mutual information. Comput Biol Med 2022;150:106145. [PMID: 37859276 DOI: 10.1016/j.compbiomed.2022.106145] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/23/2022] [Accepted: 09/24/2022] [Indexed: 11/03/2022]
35
Manish M, Mishra S, Anand A, Subbarao N. Computational molecular interaction between SARS-CoV-2 main protease and theaflavin digallate using free energy perturbation and molecular dynamics. Comput Biol Med 2022;150:106125. [PMID: 36240593 PMCID: PMC9507791 DOI: 10.1016/j.compbiomed.2022.106125] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 09/10/2022] [Accepted: 09/18/2022] [Indexed: 12/04/2022]
36
Sun X, Zhang Y, Li H, Zhou Y, Shi S, Chen Z, He X, Zhang H, Li F, Yin J, Mou M, Wang Y, Qiu Y, Zhu F. DRESIS: the first comprehensive landscape of drug resistance information. Nucleic Acids Res 2022;51:D1263-D1275. [PMID: 36243960 PMCID: PMC9825618 DOI: 10.1093/nar/gkac812] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/22/2022] [Accepted: 10/11/2022] [Indexed: 01/30/2023]  Open
37
Li F, Yin J, Lu M, Mou M, Li Z, Zeng Z, Tan Y, Wang S, Chu X, Dai H, Hou T, Zeng S, Chen Y, Zhu F. DrugMAP: molecular atlas and pharma-information of all drugs. Nucleic Acids Res 2022;51:D1288-D1299. [PMID: 36243961 PMCID: PMC9825453 DOI: 10.1093/nar/gkac813] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/30/2022] [Accepted: 10/12/2022] [Indexed: 02/06/2023]  Open
38
Yu YX, Wang W, Sun HB, Zhang LL, Wang LF, Yin YY. Decoding drug resistant mechanism of V32I, I50V and I84V mutations of HIV-1 protease on amprenavir binding by using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022;33:805-831. [PMID: 36322686 DOI: 10.1080/1062936x.2022.2140708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
39
Agrawal S, Pathak E, Mishra R, Mishra V, Parveen A, Mishra SK, Byadgi PS, Dubey SK, Chaudhary AK, Singh V, Chaurasia RN, Atri N. Computational exploration of the dual role of the phytochemical fortunellin: Antiviral activities against SARS-CoV-2 and immunomodulatory abilities against the host. Comput Biol Med 2022;149:106049. [PMID: 36103744 PMCID: PMC9452420 DOI: 10.1016/j.compbiomed.2022.106049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 01/18/2023]
40
Yu Z, Su H, Chen J, Hu G. Deciphering Conformational Changes of the GDP-Bound NRAS Induced by Mutations G13D, Q61R, and C118S through Gaussian Accelerated Molecular Dynamic Simulations. Molecules 2022;27:5596. [PMID: 36080363 PMCID: PMC9457619 DOI: 10.3390/molecules27175596] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022]  Open
41
Chen J, Wang J, Zeng Q, Wang W, Sun H, Wei B. Exploring the deactivation mechanism of human β2 adrenergic receptor by accelerated molecular dynamic simulations. Front Mol Biosci 2022;9:972463. [PMID: 36111136 PMCID: PMC9468641 DOI: 10.3389/fmolb.2022.972463] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022]  Open
42
Contractor D, Globisch C, Swaroop S, Jain A. Structural basis of Omicron immune evasion: A comparative computational study. Comput Biol Med 2022;147:105758. [PMID: 35763933 PMCID: PMC9212419 DOI: 10.1016/j.compbiomed.2022.105758] [Citation(s) in RCA: 2] [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: 04/09/2022] [Revised: 06/10/2022] [Accepted: 06/18/2022] [Indexed: 11/22/2022]
43
Bayani F, Safaei Hashkavaei N, Uversky VN, Mozaffari-Jovin S, Sefidbakht Y. Insights into the structural peculiarities of the N-terminal and receptor binding domains of the spike protein from the SARS-CoV-2 Omicron variant. Comput Biol Med 2022;147:105735. [PMID: 35767919 PMCID: PMC9220253 DOI: 10.1016/j.compbiomed.2022.105735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/26/2022] [Accepted: 06/11/2022] [Indexed: 11/03/2022]
44
Design, Synthesis, and biological evaluation of HDAC6 inhibitors based on Cap modification strategy. Bioorg Chem 2022;125:105874. [DOI: 10.1016/j.bioorg.2022.105874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/05/2022] [Accepted: 05/11/2022] [Indexed: 11/22/2022]
45
Zhang S, Sun X, Mou M, Amahong K, Sun H, Zhang W, Shi S, Li Z, Gao J, Zhu F. REGLIV: Molecular regulation data of diverse living systems facilitating current multiomics research. Comput Biol Med 2022;148:105825. [PMID: 35872412 DOI: 10.1016/j.compbiomed.2022.105825] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/29/2022] [Accepted: 07/03/2022] [Indexed: 12/24/2022]
46
Xie J, Chen R, Wang Q, Mao H. Exploration and validation of Taraxacum mongolicum anti-cancer effect. Comput Biol Med 2022;148:105819. [PMID: 35810695 DOI: 10.1016/j.compbiomed.2022.105819] [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: 04/01/2022] [Revised: 06/28/2022] [Accepted: 07/03/2022] [Indexed: 11/03/2022]
47
Khan A, Li W, Ambreen A, Wei DQ, Wang Y, Mao Y. A protein coupling and molecular simulation analysis of the clinical mutants of androgen receptor revealed a higher binding for Leupaxin, to increase the prostate cancer invasion and motility. Comput Biol Med 2022;146:105537. [DOI: 10.1016/j.compbiomed.2022.105537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 12/19/2022]
48
Damale MG, Patil R, Ansari SA, Alkahtani HM, Ahmed S, Nur-e-Alam M, Arote R, Sangshetti J. Insilico structure based drug design approach to find potential hits in ventilator-associated pneumonia caused by Pseudomonas aeruginosa. Comput Biol Med 2022;146:105597. [DOI: 10.1016/j.compbiomed.2022.105597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022]
49
Singh R, Bhardwaj VK, Das P, Bhattacherjee D, Zyryanov GV, Purohit R. Benchmarking the ability of novel compounds to inhibit SARS-CoV-2 main protease using steered molecular dynamics simulations. Comput Biol Med 2022;146:105572. [PMID: 35551011 PMCID: PMC9052739 DOI: 10.1016/j.compbiomed.2022.105572] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/31/2023]
50
Nag A, Banerjee R, Paul S, Kundu R. Curcumin inhibits spike protein of new SARS-CoV-2 variant of concern (VOC) Omicron, an in silico study. Comput Biol Med 2022;146:105552. [PMID: 35508082 PMCID: PMC9044632 DOI: 10.1016/j.compbiomed.2022.105552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/17/2022] [Accepted: 04/20/2022] [Indexed: 01/17/2023]
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