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For: Kurkcuoglu O, Jernigan RL, Doruker P. Loop motions of triosephosphate isomerase observed with elastic networks. Biochemistry 2006;45:1173-82. [PMID: 16430213 PMCID: PMC2556966 DOI: 10.1021/bi0518085] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
Mailhot O, Frappier V, Major F, Najmanovich RJ. Sequence-sensitive elastic network captures dynamical features necessary for miR-125a maturation. PLoS Comput Biol 2022;18:e1010777. [PMID: 36516216 PMCID: PMC9797095 DOI: 10.1371/journal.pcbi.1010777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/28/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]  Open
2
Kaynak BT, Krieger JM, Dudas B, Dahmani ZL, Costa MGS, Balog E, Scott AL, Doruker P, Perahia D, Bahar I. Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods. Front Mol Biosci 2022;9:832847. [PMID: 35187088 PMCID: PMC8855042 DOI: 10.3389/fmolb.2022.832847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/12/2022] [Indexed: 12/17/2022]  Open
3
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: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
4
Kulkarni YS, Amyes TL, Richard JP, Kamerlin SCL. Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase. J Am Chem Soc 2019;141:16139-16150. [PMID: 31508957 PMCID: PMC7032883 DOI: 10.1021/jacs.9b08713] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
5
Frezza E, Lavery R. Internal Coordinate Normal Mode Analysis: A Strategy To Predict Protein Conformational Transitions. J Phys Chem B 2019;123:1294-1301. [DOI: 10.1021/acs.jpcb.8b11913] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
6
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: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
7
Song G. Symmetry in normal modes and its strong dependence on symmetry in structure. J Mol Graph Model 2017;75:32-41. [DOI: 10.1016/j.jmgm.2017.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 10/19/2022]
8
Mishra SK, Sankar K, Jernigan RL. Altered dynamics upon oligomerization corresponds to key functional sites. Proteins 2017;85:1422-1434. [PMID: 28383162 DOI: 10.1002/prot.25302] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/03/2017] [Indexed: 12/18/2022]
9
Kurkcuoglu Z, Bahar I, Doruker P. ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution. J Chem Theory Comput 2016;12:4549-62. [PMID: 27494296 DOI: 10.1021/acs.jctc.6b00319] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
10
Tiwari SP, Reuter N. Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes. PLoS Comput Biol 2016;12:e1004834. [PMID: 27015412 PMCID: PMC4807811 DOI: 10.1371/journal.pcbi.1004834] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/25/2016] [Indexed: 11/19/2022]  Open
11
Zhao ZW, Xie XS, Ge H. Nonequilibrium Relaxation of Conformational Dynamics Facilitates Catalytic Reaction in an Elastic Network Model of T7 DNA Polymerase. J Phys Chem B 2016;120:2869-77. [PMID: 26918464 DOI: 10.1021/acs.jpcb.5b11002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
12
Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016;116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
13
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: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/08/2015] [Indexed: 11/24/2022]  Open
14
Frezza E, Lavery R. Internal Normal Mode Analysis (iNMA) Applied to Protein Conformational Flexibility. J Chem Theory Comput 2015;11:5503-12. [DOI: 10.1021/acs.jctc.5b00724] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
15
Kurkcuoglu Z, Findik D, Akten ED, Doruker P. How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics. Biophys J 2015;109:1169-78. [PMID: 26190635 DOI: 10.1016/j.bpj.2015.06.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/18/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022]  Open
16
The performance of fine-grained and coarse-grained elastic network models and its dependence on various factors. Proteins 2015;83:1273-83. [DOI: 10.1002/prot.24819] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/10/2015] [Accepted: 04/17/2015] [Indexed: 11/07/2022]
17
Sim J, Sim J, Park E, Lee J. Method for identification of rigid domains and hinge residues in proteins based on exhaustive enumeration. Proteins 2015;83:1054-67. [DOI: 10.1002/prot.24799] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/28/2015] [Accepted: 03/10/2015] [Indexed: 11/07/2022]
18
Na H, Song G. Conventional NMA as a better standard for evaluating elastic network models. Proteins 2014;83:259-67. [DOI: 10.1002/prot.24735] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/14/2014] [Accepted: 11/26/2014] [Indexed: 11/08/2022]
19
Na H, Song G. Bridging between normal mode analysis and elastic network models. Proteins 2014;82:2157-68. [DOI: 10.1002/prot.24571] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 03/06/2014] [Accepted: 03/21/2014] [Indexed: 11/10/2022]
20
Frappier V, Najmanovich RJ. A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations. PLoS Comput Biol 2014;10:e1003569. [PMID: 24762569 PMCID: PMC3998880 DOI: 10.1371/journal.pcbi.1003569] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/25/2014] [Indexed: 11/18/2022]  Open
21
Katebi AR, Jernigan RL. The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality. Protein Sci 2013;23:213-28. [PMID: 24318986 DOI: 10.1002/pro.2407] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 12/01/2013] [Accepted: 12/03/2013] [Indexed: 11/11/2022]
22
Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase. ENTROPY 2013. [DOI: 10.3390/e15031085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
23
Micheletti C. Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments. Phys Life Rev 2012. [PMID: 23199577 DOI: 10.1016/j.plrev.2012.10.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
24
Kurkcuoglu Z, Bakan A, Kocaman D, Bahar I, Doruker P. Coupling between catalytic loop motions and enzyme global dynamics. PLoS Comput Biol 2012;8:e1002705. [PMID: 23028297 PMCID: PMC3459879 DOI: 10.1371/journal.pcbi.1002705] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 08/02/2012] [Indexed: 11/18/2022]  Open
25
Skliros A, Zimmermann MT, Chakraborty D, Saraswathi S, Katebi AR, Leelananda SP, Kloczkowski A, Jernigan RL. The importance of slow motions for protein functional loops. Phys Biol 2012;9:014001. [PMID: 22314977 DOI: 10.1088/1478-3975/9/1/014001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
26
Uyar A, Kurkcuoglu O, Nilsson L, Doruker P. The elastic network model reveals a consistent picture on intrinsic functional dynamics of type II restriction endonucleases. Phys Biol 2011;8:056001. [PMID: 21791727 DOI: 10.1088/1478-3975/8/5/056001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
27
Ahmed A, Rippmann F, Barnickel G, Gohlke H. A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins. J Chem Inf Model 2011;51:1604-22. [PMID: 21639141 DOI: 10.1021/ci100461k] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
28
Role of loop dynamics in thermal stability of mesophilic and thermophilic adenylosuccinate synthetase: a molecular dynamics and normal mode analysis study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011;1814:630-7. [PMID: 21440684 DOI: 10.1016/j.bbapap.2011.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 02/19/2011] [Accepted: 03/18/2011] [Indexed: 01/28/2023]
29
Markwick PRL, McCammon JA. Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Phys Chem Chem Phys 2011;13:20053-65. [DOI: 10.1039/c1cp22100k] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
30
Moal IH, Bates PA. SwarmDock and the use of normal modes in protein-protein docking. Int J Mol Sci 2010;11:3623-48. [PMID: 21152290 PMCID: PMC2996808 DOI: 10.3390/ijms11103623] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 07/29/2010] [Accepted: 09/16/2010] [Indexed: 11/17/2022]  Open
31
Ozer N, Schiffer CA, Haliloglu T. Rationale for more diverse inhibitors in competition with substrates in HIV-1 protease. Biophys J 2010;99:1650-9. [PMID: 20816079 PMCID: PMC2931728 DOI: 10.1016/j.bpj.2010.06.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 06/25/2010] [Accepted: 06/28/2010] [Indexed: 11/29/2022]  Open
32
Martins M, Ferreira S, Vilela M. Multiscale models for biological systems. Curr Opin Colloid Interface Sci 2010. [DOI: 10.1016/j.cocis.2009.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
33
Bahar I, Lezon TR, Bakan A, Shrivastava IH. Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins. Chem Rev 2010;110:1463-97. [PMID: 19785456 PMCID: PMC2836427 DOI: 10.1021/cr900095e] [Citation(s) in RCA: 393] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
34
Kurkcuoglu O, Turgut OT, Cansu S, Jernigan RL, Doruker P. Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model. Biophys J 2009;97:1178-87. [PMID: 19686666 DOI: 10.1016/j.bpj.2009.06.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 05/12/2009] [Accepted: 06/01/2009] [Indexed: 01/03/2023]  Open
35
Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci U S A 2009;106:12347-52. [PMID: 19617554 DOI: 10.1073/pnas.0902159106] [Citation(s) in RCA: 195] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
36
Ho BK, Agard DA. Probing the flexibility of large conformational changes in protein structures through local perturbations. PLoS Comput Biol 2009;5:e1000343. [PMID: 19343225 PMCID: PMC2660149 DOI: 10.1371/journal.pcbi.1000343] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 02/27/2009] [Indexed: 11/19/2022]  Open
37
Delarue M. Dealing with structural variability in molecular replacement and crystallographic refinement through normal-mode analysis. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2007;64:40-8. [PMID: 18094466 PMCID: PMC2394787 DOI: 10.1107/s0907444907053516] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Accepted: 10/26/2007] [Indexed: 01/08/2023]
38
Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation. Curr Opin Struct Biol 2007;17:633-40. [PMID: 18024008 DOI: 10.1016/j.sbi.2007.09.011] [Citation(s) in RCA: 248] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 08/21/2007] [Accepted: 09/28/2007] [Indexed: 11/23/2022]
39
Olivares-Illana V, Rodríguez-Romero A, Becker I, Berzunza M, García J, Pérez-Montfort R, Cabrera N, López-Calahorra F, de Gómez-Puyou MT, Gómez-Puyou A. Perturbation of the dimer interface of triosephosphate isomerase and its effect on Trypanosoma cruzi. PLoS Negl Trop Dis 2007;1:e1. [PMID: 17989778 PMCID: PMC2041813 DOI: 10.1371/journal.pntd.0000001] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2007] [Accepted: 06/07/2007] [Indexed: 11/18/2022]  Open
40
Sacquin-Mora S, Laforet E, Lavery R. Locating the active sites of enzymes using mechanical properties. Proteins 2007;67:350-9. [PMID: 17311346 DOI: 10.1002/prot.21353] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
41
Zomosa-Signoret V, Aguirre-López B, Hernández-Alcántara G, Pérez-Montfort R, de Gómez-Puyou MT, Gómez-Puyou A. Crosstalk between the subunits of the homodimeric enzyme triosephosphate isomerase. Proteins 2007;67:75-83. [PMID: 17221869 DOI: 10.1002/prot.21242] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
42
Amyes TL, Richard JP. Enzymatic catalysis of proton transfer at carbon: activation of triosephosphate isomerase by phosphite dianion. Biochemistry 2007;46:5841-54. [PMID: 17444661 PMCID: PMC2556868 DOI: 10.1021/bi700409b] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
43
Ayton GS, Noid WG, Voth GA. Multiscale modeling of biomolecular systems: in serial and in parallel. Curr Opin Struct Biol 2007;17:192-8. [PMID: 17383173 DOI: 10.1016/j.sbi.2007.03.004] [Citation(s) in RCA: 305] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Revised: 02/21/2007] [Accepted: 03/13/2007] [Indexed: 02/07/2023]
44
Doruker P, Nilsson L, Kurkcuoglu O. Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations. J Biomol Struct Dyn 2006;24:1-16. [PMID: 16780370 DOI: 10.1080/07391102.2006.10507093] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
45
Sen TZ, Feng Y, Garcia JV, Kloczkowski A, Jernigan RL. The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models. J Chem Theory Comput 2006;2:696-704. [PMID: 17710199 PMCID: PMC1948848 DOI: 10.1021/ct600060d] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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