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For: Dehury B, Maharana J, Sahoo BR, Sahu J, Sen P, Modi MK, Barooah M. Molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (Oryza sativa L.): insights from molecular dynamics simulations. J Mol Graph Model 2015;57:49-61. [PMID: 25655560 DOI: 10.1016/j.jmgm.2015.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/06/2014] [Accepted: 01/09/2015] [Indexed: 11/17/2022]
Number Cited by Other Article(s)
1
Mishra S, Rout M, Singh MK, Dehury B, Pati S. Classical molecular dynamics simulation identifies catechingallate as a promising antiviral polyphenol against MPOX palmitoylated surface protein. Comput Biol Chem 2024;110:108070. [PMID: 38678726 DOI: 10.1016/j.compbiolchem.2024.108070] [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: 01/24/2024] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 05/01/2024]
2
Dehury B, Raina V, Misra N, Suar M. Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study. J Biomol Struct Dyn 2020;39:7231-7245. [PMID: 32762417 PMCID: PMC7484587 DOI: 10.1080/07391102.2020.1802348] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
4
Dikhit MR, Das S, Mahantesh V, Kumar A, Singh AK, Dehury B, Rout AK, Ali V, Sahoo GC, Topno RK, Pandey K, Das VNR, Bimal S, Das P. The potential HLA Class I-restricted epitopes derived from LeIF and TSA of Leishmania donovani evoke anti-leishmania CD8+ T lymphocyte response. Sci Rep 2018;8:14175. [PMID: 30242172 PMCID: PMC6154976 DOI: 10.1038/s41598-018-32040-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 08/14/2018] [Indexed: 12/12/2022]  Open
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: 345] [Impact Index Per Article: 57.5] [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
Generation of dTALEs and Libraries of Synthetic TALE-Activated Promoters for Engineering of Gene Regulatory Networks in Plants. Methods Mol Biol 2017. [PMID: 28623587 DOI: 10.1007/978-1-4939-7125-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
7
Streubel J, Baum H, Grau J, Stuttman J, Boch J. Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations. PLoS One 2017;12:e0173580. [PMID: 28301511 PMCID: PMC5354296 DOI: 10.1371/journal.pone.0173580] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/22/2017] [Indexed: 11/19/2022]  Open
8
Structural dynamics of Casein Kinase I (CKI) from malarial parasite Plasmodium falciparum (Isolate 3D7): Insights from theoretical modelling and molecular simulations. J Mol Graph Model 2016;71:154-166. [PMID: 27923179 DOI: 10.1016/j.jmgm.2016.11.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/24/2016] [Accepted: 11/18/2016] [Indexed: 12/21/2022]
9
Harish Vagadia B, Vanga SK, Singh A, Raghavan V. Effects of thermal and electric fields on soybean trypsin inhibitor protein: A molecular modelling study. INNOV FOOD SCI EMERG 2016. [DOI: 10.1016/j.ifset.2016.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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