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Number Cited by Other Article(s)
1
Gülbakan B, Barylyuk K, Schneider P, Pillong M, Schneider G, Zenobi R. Native Electrospray Ionization Mass Spectrometry Reveals Multiple Facets of Aptamer–Ligand Interactions: From Mechanism to Binding Constants. J Am Chem Soc 2018;140:7486-7497. [DOI: 10.1021/jacs.7b13044] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
2
Ding JN, Zhang YJ, Zhong H, Ao CC, Han JG. A simulation investigation on interaction mechanism between Ebola nucleoprotein and VP35 peptide. J Biomol Struct Dyn 2018;36:1009-1028. [DOI: 10.1080/07391102.2017.1307143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
3
Ding JN, Zhang YJ, Zhong H, Ao CC, Li J, Han JG. An all-atom molecular dynamics study of the anti-interferon signaling of Ebola virus: interaction mechanisms of EBOV VP24 binding to Karyopherin alpha5. MOLECULAR BIOSYSTEMS 2018;13:1031-1045. [PMID: 28418440 DOI: 10.1039/c7mb00136c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
4
Mou L, Cui T, Liu W, Zhang H, Cai Z, Lu S, Gao G. Microsecond molecular dynamics simulations provide insight into the ATP-competitive inhibitor-induced allosteric protection of Akt kinase phosphorylation. Chem Biol Drug Des 2016;89:723-731. [PMID: 27797456 DOI: 10.1111/cbdd.12895] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/02/2016] [Accepted: 10/25/2016] [Indexed: 11/28/2022]
5
Xue Q, Zheng QC, Zhang JL, Cui YL, Zhang HX. Exploring the mechanism how Marburg virus VP35 recognizes and binds dsRNA by molecular dynamics simulations and free energy calculations. Biopolymers 2016;101:849-60. [PMID: 24459115 DOI: 10.1002/bip.22463] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/16/2014] [Accepted: 01/17/2014] [Indexed: 12/14/2022]
6
Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis. Sci Rep 2016;6:24587. [PMID: 27079666 PMCID: PMC4832343 DOI: 10.1038/srep24587] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 03/31/2016] [Indexed: 01/19/2023]  Open
7
Wu J, Ye W, Yang J, Chen HF. Conformational selection and induced fit for RNA polymerase and RNA/DNA hybrid backtracked recognition. Front Mol Biosci 2015;2:61. [PMID: 26594643 PMCID: PMC4633505 DOI: 10.3389/fmolb.2015.00061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/11/2015] [Indexed: 01/22/2023]  Open
8
Binding Induced Intrinsically Disordered Protein Folding with Molecular Dynamics Simulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015;827:111-21. [DOI: 10.1007/978-94-017-9245-5_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
9
Chen T, Song J, Chan HS. Theoretical perspectives on nonnative interactions and intrinsic disorder in protein folding and binding. Curr Opin Struct Biol 2014;30:32-42. [PMID: 25544254 DOI: 10.1016/j.sbi.2014.12.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/02/2014] [Accepted: 12/02/2014] [Indexed: 11/29/2022]
10
Ye W, Yang J, Yu Q, Wang W, Hancy J, Luo R, Chen HF. Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations. Phys Chem Chem Phys 2014;15:18510-22. [PMID: 24072031 DOI: 10.1039/c3cp53145g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
11
Tayal N, Choudhary P, Pandit SB, Sandhu KS. Evolutionarily conserved and conformationally constrained short peptides might serve as DNA recognition elements in intrinsically disordered regions. MOLECULAR BIOSYSTEMS 2014;10:1469-80. [PMID: 24668165 DOI: 10.1039/c3mb70539k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
12
Xue Q, Zhang JL, Zheng QC, Cui YL, Chen L, Chu WT, Zhang HX. Exploring the molecular basis of dsRNA recognition by Mss116p using molecular dynamics simulations and free-energy calculations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013;29:11135-11144. [PMID: 23895307 DOI: 10.1021/la402354r] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
13
Baker CM, Best RB. Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013;4:182-198. [PMID: 34354764 DOI: 10.1002/wcms.1167] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
14
Atomistic mechanism of microRNA translation upregulation via molecular dynamics simulations. PLoS One 2012;7:e43788. [PMID: 22952765 PMCID: PMC3428290 DOI: 10.1371/journal.pone.0043788] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 07/24/2012] [Indexed: 01/16/2023]  Open
15
Ye W, Chen Y, Wang W, Yu Q, Li Y, Zhang J, Chen HF. Insight into the stability of cross-β amyloid fibril from VEALYL short peptide with molecular dynamics simulation. PLoS One 2012;7:e36382. [PMID: 22590535 PMCID: PMC3349666 DOI: 10.1371/journal.pone.0036382] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 03/30/2012] [Indexed: 12/13/2022]  Open
16
Yan GW, Chen Y, Li Y, Chen HF. Revealing interaction mode between HIV-1 protease and mannitol analog inhibitor. Chem Biol Drug Des 2012;79:916-25. [PMID: 22296911 DOI: 10.1111/j.1747-0285.2012.01348.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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