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For: Na H, Jernigan RL, Song G. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models. PLoS Comput Biol 2015;11:e1004542. [PMID: 26473491 PMCID: PMC4608564 DOI: 10.1371/journal.pcbi.1004542] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/08/2015] [Indexed: 11/24/2022]  Open
Number Cited by Other Article(s)
1
Na H, Song G. Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters' Hydrogens. J Chem Theory Comput 2023;19:7307-7323. [PMID: 37782694 PMCID: PMC10601925 DOI: 10.1021/acs.jctc.3c00700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Indexed: 10/04/2023]
2
Khan MW, Murali A. Normal mode analysis and comparative study of intrinsic dynamics of alcohol oxidase enzymes from GMC protein family. J Biomol Struct Dyn 2023;42:10075-10090. [PMID: 37676256 DOI: 10.1080/07391102.2023.2255275] [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: 06/09/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
3
Anand DV, Wei RKJ, Xia K. Coarse-Grained Models for Vault Normal Model Analysis. Methods Mol Biol 2023;2671:307-318. [PMID: 37308652 DOI: 10.1007/978-1-0716-3222-2_17] [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: 06/14/2023]
4
Zhang H, Shan G, Yang B. Optimized Elastic Network Models With Direct Characterization of Inter-Residue Cooperativity for Protein Dynamics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:1064-1074. [PMID: 32915744 DOI: 10.1109/tcbb.2020.3023147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
5
A Comparative Evaluation of the Structural and Dynamic Properties of Insect Odorant Binding Proteins. Biomolecules 2022;12:biom12020282. [PMID: 35204784 PMCID: PMC8961588 DOI: 10.3390/biom12020282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 02/01/2023]  Open
6
Modal Analysis of the Lysozyme Protein Considering All-Atom and Coarse-Grained Finite Element Models. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11020547] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
7
Wang S, Gong W, Deng X, Liu Y, Li C. Exploring the dynamics of RNA molecules with multiscale Gaussian network model. Chem Phys 2020. [DOI: 10.1016/j.chemphys.2020.110820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
8
Bose Majumdar A, Kim IJ, Na H. Effect of solvent on protein structure and dynamics. Phys Biol 2020;17:036006. [DOI: 10.1088/1478-3975/ab74b3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
9
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: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
10
Anand DV, Meng Z, Xia K. A complex multiscale virtual particle model based elastic network model (CMVP-ENM) for the normal mode analysis of biomolecular complexes. Phys Chem Chem Phys 2019;21:4359-4366. [DOI: 10.1039/c8cp07442a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
11
Song G. A time and memory efficient recipe for fast normal mode computations of complexes with icosahedral symmetry. J Mol Graph Model 2018;87:30-40. [PMID: 30476733 DOI: 10.1016/j.jmgm.2018.10.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/22/2018] [Accepted: 10/24/2018] [Indexed: 11/26/2022]
12
Budday D, Leyendecker S, van den Bedem H. Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion. J Chem Inf Model 2018;58:2108-2122. [PMID: 30240209 DOI: 10.1021/acs.jcim.8b00267] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
13
Na H, Song G. All-atom normal mode dynamics of HIV-1 capsid. PLoS Comput Biol 2018;14:e1006456. [PMID: 30226840 PMCID: PMC6161923 DOI: 10.1371/journal.pcbi.1006456] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/28/2018] [Accepted: 08/22/2018] [Indexed: 01/25/2023]  Open
14
Yu M, Ma X, Cao H, Chong B, Lai L, Liu Z. Singular value decomposition for the correlation of atomic fluctuations with arbitrary angle. Proteins 2018;86:1075-1087. [PMID: 30019778 DOI: 10.1002/prot.25586] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/22/2018] [Accepted: 07/04/2018] [Indexed: 01/21/2023]
15
Na H, Song G. Fast Normal Mode Computations of Capsid Dynamics Inspired by Resonance. Phys Biol 2018;15:046003. [PMID: 29557348 DOI: 10.1088/1478-3975/aab813] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
16
Xia K. Multiscale virtual particle based elastic network model (MVP-ENM) for normal mode analysis of large-sized biomolecules. Phys Chem Chem Phys 2018;20:658-669. [PMID: 29227479 DOI: 10.1039/c7cp07177a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
17
Computational Methods for Efficient Sampling of Protein Landscapes and Disclosing Allosteric Regions. COMPUTATIONAL MOLECULAR MODELLING IN STRUCTURAL BIOLOGY 2018;113:33-63. [DOI: 10.1016/bs.apcsb.2018.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
18
Dong Z, Zhou H, Tao P. Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily. Protein Sci 2017;27:421-430. [PMID: 29052279 DOI: 10.1002/pro.3329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 10/10/2017] [Accepted: 10/15/2017] [Indexed: 11/11/2022]
19
Gaussian network model can be enhanced by combining solvent accessibility in proteins. Sci Rep 2017;7:7486. [PMID: 28790346 PMCID: PMC5548781 DOI: 10.1038/s41598-017-07677-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 06/29/2017] [Indexed: 01/03/2023]  Open
20
Koehl P, Poitevin F, Navaza R, Delarue M. The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems. J Chem Theory Comput 2017;13:1424-1438. [PMID: 28170254 DOI: 10.1021/acs.jctc.6b01136] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
21
Hsieh YC, Poitevin F, Delarue M, Koehl P. Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids. Front Mol Biosci 2016;3:85. [PMID: 28083537 PMCID: PMC5187361 DOI: 10.3389/fmolb.2016.00085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/12/2016] [Indexed: 11/13/2022]  Open
22
Na H, Song G. Predicting the functional motions of p97 using symmetric normal modes. Proteins 2016;84:1823-1835. [PMID: 27653958 DOI: 10.1002/prot.25164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/09/2016] [Accepted: 09/15/2016] [Indexed: 01/01/2023]
23
DeWolf T, Gordon R. Theory of Acoustic Raman Modes in Proteins. PHYSICAL REVIEW LETTERS 2016;117:138101. [PMID: 27715080 DOI: 10.1103/physrevlett.117.138101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Indexed: 05/23/2023]
24
Ma X, Meng H, Lai L. Motions of Allosteric and Orthosteric Ligand-Binding Sites in Proteins are Highly Correlated. J Chem Inf Model 2016;56:1725-33. [DOI: 10.1021/acs.jcim.6b00039] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
25
O'Rourke KF, Gorman SD, Boehr DD. Biophysical and computational methods to analyze amino acid interaction networks in proteins. Comput Struct Biotechnol J 2016;14:245-51. [PMID: 27441044 PMCID: PMC4939391 DOI: 10.1016/j.csbj.2016.06.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/04/2016] [Accepted: 06/13/2016] [Indexed: 12/20/2022]  Open
26
Na H, Song G. The effective degeneracy of protein normal modes. Phys Biol 2016;13:036002. [DOI: 10.1088/1478-3975/13/3/036002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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