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For: Sahoo BR, Dubey PK, Goyal S, Bhoi GK, Lenka SK, Maharana J, Pradhan SK, Kataria RS. Exploration of the binding modes of buffalo PGRP1 receptor complexed with meso-diaminopimelic acid and lysine-type peptidoglycans by molecular dynamics simulation and free energy calculation. Chem Biol Interact 2014;220:255-68. [PMID: 25014416 DOI: 10.1016/j.cbi.2014.06.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/28/2014] [Accepted: 06/30/2014] [Indexed: 12/20/2022]
Number Cited by Other Article(s)
1
Xu N, Wang Z, Xu Z, Zhang X, Jin Z, Dong X, Lin D. Experimentally verified flexible molecular docking and dynamic simulation of aptamer with intracellular proteins based on direct DNA 3D structure prediction. Int J Biol Macromol 2025;316:144318. [PMID: 40383336 DOI: 10.1016/j.ijbiomac.2025.144318] [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: 12/23/2024] [Revised: 04/19/2025] [Accepted: 05/15/2025] [Indexed: 05/20/2025]
2
Sahoo BR, Bekier ME, Liu Z, Kocman V, Stoddard AK, Anantharamaiah GM, Nowick J, Fierke CA, Wang Y, Ramamoorthy A. Structural Interaction of Apolipoprotein A-I Mimetic Peptide with Amyloid-β Generates Toxic Hetero-oligomers. J Mol Biol 2019;432:1020-1034. [PMID: 31866295 DOI: 10.1016/j.jmb.2019.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 01/21/2023]
3
Rout AK, Paramanik S, Dehury B, Acharya V, Swain HS, Pradhan SK, Behera B, Pati SK, Behera BK, Das BK. Elucidating the molecular interaction of Zebrafish (Danio rerio) peptidoglycan recognition protein 2 with diaminopimelic acid and lysine type peptidoglycans using in silico approaches. J Biomol Struct Dyn 2019;38:3687-3699. [DOI: 10.1080/07391102.2019.1666742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
4
Bitencourt-Ferreira G, de Azevedo WF. Molecular Docking Simulations with ArgusLab. Methods Mol Biol 2019;2053:203-220. [PMID: 31452107 DOI: 10.1007/978-1-4939-9752-7_13] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
5
Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018;4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 399] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022]  Open
6
Characterization of the ligand binding of PGRP-L in half-smooth tongue sole ( Cynoglossus semilaevis ) by molecular dynamics and free energy calculation. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
7
Sahoo BR, Fujiwara T. Conformational states of HAMP domains interacting with sensory rhodopsin membrane systems: an integrated all-atom and coarse-grained molecular dynamics simulation approach. MOLECULAR BIOSYSTEMS 2017;13:193-207. [PMID: 27901172 DOI: 10.1039/c6mb00730a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
8
Qi Z, Meng F, Zhang Q, Wang Z, Qiao G, Xu W, Shao R, Chen C. Structural insights into ligand binding of PGRP1 splice variants in Chinese giant salamander (Andrias davidianus) from molecular dynamics and free energy calculations. J Mol Model 2017;23:135. [PMID: 28341996 DOI: 10.1007/s00894-017-3315-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/13/2017] [Indexed: 11/24/2022]
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