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For: Zou Y, Ewalt J, Ng HL. Recent Insights from Molecular Dynamics Simulations for G Protein-Coupled Receptor Drug Discovery. Int J Mol Sci 2019;20:E4237. [PMID: 31470676 PMCID: PMC6747122 DOI: 10.3390/ijms20174237] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]  Open
Number Cited by Other Article(s)
1
Vásquez E, Oresti GM, Paez MD, Callegari EA, Masone D, Muñoz EM. Impact of aging on the GABAB receptor-mediated connectome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.606013. [PMID: 39131332 PMCID: PMC11312617 DOI: 10.1101/2024.07.31.606013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
2
Alananzeh WA, Al-Qattan MN, Ayipo YO, Mordi MN. N-substituted tetrahydro-beta-carboline as mu-opioid receptors ligands: in silico study; molecular docking, ADMET and molecular dynamics approach. Mol Divers 2024;28:1273-1289. [PMID: 37133710 DOI: 10.1007/s11030-023-10655-1] [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: 01/26/2023] [Accepted: 04/20/2023] [Indexed: 05/04/2023]
3
Calderón JC, Ibrahim P, Gobbo D, Gervasio FL, Clark T. Determinants of Neutral Antagonism and Inverse Agonism in the β2-Adrenergic Receptor. J Chem Inf Model 2024;64:2045-2057. [PMID: 38447156 DOI: 10.1021/acs.jcim.3c01763] [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: 03/08/2024]
4
Kožić M, Bertoša B. Trajectory maps: molecular dynamics visualization and analysis. NAR Genom Bioinform 2024;6:lqad114. [PMID: 38226394 PMCID: PMC10789246 DOI: 10.1093/nargab/lqad114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/01/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]  Open
5
Menchon G, Maveyraud L, Czaplicki G. Molecular Dynamics as a Tool for Virtual Ligand Screening. Methods Mol Biol 2024;2714:33-83. [PMID: 37676592 DOI: 10.1007/978-1-0716-3441-7_3] [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] [Indexed: 09/08/2023]
6
Bueschbell B, Magalhães PR, Barreto CA, Melo R, Schiedel AC, Machuqueiro M, Moreira IS. The World of GPCR dimers - Mapping dopamine receptor D2 homodimers in different activation states and configuration arrangements. Comput Struct Biotechnol J 2023;21:4336-4353. [PMID: 37711187 PMCID: PMC10497915 DOI: 10.1016/j.csbj.2023.08.032] [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: 04/25/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023]  Open
7
Identification of Dietary Bioflavonoids as Potential Inhibitors against KRAS G12D Mutant—Novel Insights from Computer-Aided Drug Discovery. Curr Issues Mol Biol 2023;45:2136-2156. [PMID: 36975507 PMCID: PMC10047893 DOI: 10.3390/cimb45030137] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/08/2023]  Open
8
Shi M, Zhou Y, Wei H, Zhang X, Du M, Zhou Y, Yin Y, Li X, Tang X, Sun L, Xu D, Li X. Interactions between curcumin and human salt-induced kinase 3 elucidated from computational tools and experimental methods. Front Pharmacol 2023;14:1116098. [PMID: 37124223 PMCID: PMC10133576 DOI: 10.3389/fphar.2023.1116098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/03/2023] [Indexed: 05/02/2023]  Open
9
Liu J, Guo H, Zhou J, Wang Y, Yan H, Jin R, Tang Y. Evodiamine and Rutaecarpine as Potential Anticancer Compounds: A Combined Computational Study. Int J Mol Sci 2022;23:ijms231911513. [PMID: 36232809 PMCID: PMC9570036 DOI: 10.3390/ijms231911513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/18/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2022]  Open
10
Róg T, Girych M, Bunker A. Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design. Pharmaceuticals (Basel) 2021;14:1062. [PMID: 34681286 PMCID: PMC8537670 DOI: 10.3390/ph14101062] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/17/2022]  Open
11
Mahmood MI, Yamashita T. Influence of Lipid Bilayer on the GPCR Structure: Comparison of All-Atom Lipid Force Fields. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
12
Vidad AR, Macaspac S, Ng HL. Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservation. PeerJ 2021;9:e12219. [PMID: 34631323 PMCID: PMC8475542 DOI: 10.7717/peerj.12219] [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: 09/16/2020] [Accepted: 09/06/2021] [Indexed: 11/20/2022]  Open
13
Gautam V, Nimmanpipug P, Zain SM, Rahman NA, Lee VS. Molecular Dynamics Simulations in Designing DARPins as Phosphorylation-Specific Protein Binders of ERK2. Molecules 2021;26:molecules26154540. [PMID: 34361694 PMCID: PMC8347146 DOI: 10.3390/molecules26154540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022]  Open
14
Shi M, Wang L, Li P, Liu J, Chen L, Xu D. Dasatinib-SIK2 Binding Elucidated by Homology Modeling, Molecular Docking, and Dynamics Simulations. ACS OMEGA 2021;6:11025-11038. [PMID: 34056256 PMCID: PMC8153941 DOI: 10.1021/acsomega.1c00947] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/06/2021] [Indexed: 02/08/2023]
15
Aydin Y, Coin I. Biochemical insights into structure and function of arrestins. FEBS J 2021;288:2529-2549. [DOI: 10.1111/febs.15811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022]
16
Wang H, Cao D, Gillespie JC, Mendez RE, Selley DE, Liu-Chen LY, Zhang Y. Exploring the putative mechanism of allosteric modulations by mixed-action kappa/mu opioid receptor bitopic modulators. Future Med Chem 2021;13:551-573. [PMID: 33590767 PMCID: PMC8027703 DOI: 10.4155/fmc-2020-0308] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/14/2021] [Indexed: 12/26/2022]  Open
17
Arodola OA, Kanchi S, Hloma P, Bisetty K, Asiri AM, Inamuddin. An in-silico layer-by-layer adsorption study of the interaction between Rebaudioside A and the T1R2 human sweet taste receptor: modelling and biosensing perspectives. Sci Rep 2020;10:18391. [PMID: 33110140 PMCID: PMC7591876 DOI: 10.1038/s41598-020-75123-4] [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: 02/10/2020] [Accepted: 09/28/2020] [Indexed: 12/03/2022]  Open
18
Torrens-Fontanals M, Stepniewski TM, Aranda-García D, Morales-Pastor A, Medel-Lacruz B, Selent J. How Do Molecular Dynamics Data Complement Static Structural Data of GPCRs. Int J Mol Sci 2020;21:E5933. [PMID: 32824756 PMCID: PMC7460635 DOI: 10.3390/ijms21165933] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 01/08/2023]  Open
19
GPR43 regulates HBV X protein (HBx)-induced inflammatory response in human LO2 hepatocytes. Biomed Pharmacother 2020;123:109737. [DOI: 10.1016/j.biopha.2019.109737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 11/13/2019] [Accepted: 11/27/2019] [Indexed: 12/18/2022]  Open
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