• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (5081075)   Today's Articles (1112)
For: Identification of key residues for protein conformational transition using elastic network model. J Chem Phys 2011;135:174101. [DOI: 10.1063/1.3651480] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
Number Cited by Other Article(s)
1
Zhao Y, Zhang X, Liu L, Hu F, Chang F, Han Z, Li C. Insights into Activation Dynamics and Functional Sites of Inwardly Rectifying Potassium Channel Kir3.2 by an Elastic Network Model Combined with Perturbation Methods. J Phys Chem B 2024;128:1360-1370. [PMID: 38308647 DOI: 10.1021/acs.jpcb.3c06739] [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: 02/05/2024]
2
Deng X, Wang S, Han Z, Gong W, Liu Y, Li C. Dynamics of binding interactions of TDP-43 and RNA: An equally weighted multiscale elastic network model study. Proteins 2021;90:589-600. [PMID: 34599611 DOI: 10.1002/prot.26255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023]
3
He J, Han Z, Farooq QUA, Li C. Study on functional sites in human multidrug resistance protein 1 (hMRP1). Proteins 2021;89:659-670. [PMID: 33469960 DOI: 10.1002/prot.26049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 11/22/2020] [Accepted: 12/27/2020] [Indexed: 01/27/2023]
4
Zhang PF, Su JG. Identification of key sites controlling protein functional motions by using elastic network model combined with internal coordinates. J Chem Phys 2019;151:045101. [PMID: 31370540 DOI: 10.1063/1.5098542] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
5
Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model. Biophys J 2019;116:1625-1636. [PMID: 30975455 DOI: 10.1016/j.bpj.2019.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 12/14/2022]  Open
6
Wang WB, Liang Y, Zhang J, Wu YD, Du JJ, Li QM, Zhu JZ, Su JG. Energy transport pathway in proteins: Insights from non-equilibrium molecular dynamics with elastic network model. Sci Rep 2018;8:9487. [PMID: 29934573 PMCID: PMC6015066 DOI: 10.1038/s41598-018-27745-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 06/08/2018] [Indexed: 11/28/2022]  Open
7
Lv D, Wang C, Li C, Tan J, Zhang X. An efficient perturbation method to predict the functionally key sites of glutamine binding protein. Comput Biol Chem 2016;67:62-68. [PMID: 28061385 DOI: 10.1016/j.compbiolchem.2016.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 11/09/2016] [Accepted: 12/15/2016] [Indexed: 12/16/2022]
8
Lv D, Li C, Tan J, Zhang X, Wang C, Su J. Identification of functionally key residues in maltose transporter with an elastic network model-based thermodynamic method. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1234077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
9
Saldaño TE, Monzon AM, Parisi G, Fernandez-Alberti S. Evolutionary Conserved Positions Define Protein Conformational Diversity. PLoS Comput Biol 2016;12:e1004775. [PMID: 27008419 PMCID: PMC4805271 DOI: 10.1371/journal.pcbi.1004775] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/27/2016] [Indexed: 12/18/2022]  Open
10
Li XY, Zhang JC, Zhu YY, Su JG. Domain Motions and Functionally-Key Residues of L-Alanine Dehydrogenase Revealed by an Elastic Network Model. Int J Mol Sci 2015;16:29383-97. [PMID: 26690143 PMCID: PMC4691113 DOI: 10.3390/ijms161226170] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/27/2015] [Accepted: 12/02/2015] [Indexed: 11/16/2022]  Open
11
Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD-BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate. Int J Mol Sci 2015;16:17933-51. [PMID: 26247943 PMCID: PMC4581229 DOI: 10.3390/ijms160817933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/10/2015] [Accepted: 07/20/2015] [Indexed: 11/17/2022]  Open
12
Su JG, Han XM, Zhang X, Hou YX, Zhu JZ, Wu YD. Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model. J Biomol Struct Dyn 2015;34:560-71. [DOI: 10.1080/07391102.2015.1044910] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
13
Bywater RP. Prediction of protein structural features from sequence data based on Shannon entropy and Kolmogorov complexity. PLoS One 2015;10:e0119306. [PMID: 25856073 PMCID: PMC4391790 DOI: 10.1371/journal.pone.0119306] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Accepted: 01/29/2015] [Indexed: 11/21/2022]  Open
14
Li XY, Xie F, Zhang JC, Su JG. Study, by use of coarse-grained models, of the functionally crucial residues and allosteric pathway of anesthetic regulation of the Gloeobacter violaceus ligand-gated ion channel. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014;43:623-30. [PMID: 25367560 DOI: 10.1007/s00249-014-0992-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/24/2014] [Accepted: 10/01/2014] [Indexed: 11/28/2022]
15
Su JG, Qi LS, Li CH, Zhu YY, Du HJ, Hou YX, Hao R, Wang JH. Prediction of allosteric sites on protein surfaces with an elastic-network-model-based thermodynamic method. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014;90:022719. [PMID: 25215770 DOI: 10.1103/physreve.90.022719] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Indexed: 06/03/2023]
16
de Mendonça MR, Rizzi LG, Contessoto V, Leite VBP, Alves NA. Inferring a weighted elastic network from partial unfolding with coarse-grained simulations. Proteins 2013;82:119-29. [DOI: 10.1002/prot.24381] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 06/29/2013] [Accepted: 07/12/2013] [Indexed: 11/10/2022]
17
Su JG, Du HJ, Hao R, Xu XJ, Li CH, Chen WZ, Wang CX. Identification of functionally key residues in AMPA receptor with a thermodynamic method. J Phys Chem B 2013;117:8689-96. [PMID: 23822189 DOI: 10.1021/jp402290t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
18
Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 2013;138:333-408. [PMID: 23384594 PMCID: PMC3647006 DOI: 10.1016/j.pharmthera.2013.01.016] [Citation(s) in RCA: 522] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 02/02/2023]
19
The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture. Biochem Soc Trans 2012;40:475-91. [PMID: 22616857 DOI: 10.1042/bst20120056] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
PrevPage 1 of 1 1Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA