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For: Kundu S, Sorensen DC, Phillips GN. Automatic domain decomposition of proteins by a Gaussian Network Model. Proteins 2006;57:725-33. [PMID: 15478120 DOI: 10.1002/prot.20268] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Number Cited by Other Article(s)
1
Kidder KM, Shell MS, Noid WG. Surveying the energy landscape of coarse-grained mappings. J Chem Phys 2024;160:054105. [PMID: 38310476 DOI: 10.1063/5.0182524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/28/2023] [Indexed: 02/05/2024]  Open
2
Taheri-Ledari M, Zandieh A, Shariatpanahi SP, Eslahchi C. Assignment of structural domains in proteins using diffusion kernels on graphs. BMC Bioinformatics 2022;23:369. [PMID: 36076174 PMCID: PMC9461149 DOI: 10.1186/s12859-022-04902-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/23/2022] [Indexed: 11/10/2022]  Open
3
Laine E, Grudinin S. HOPMA: Boosting Protein Functional Dynamics with Colored Contact Maps. J Phys Chem B 2021;125:2577-2588. [PMID: 33687221 DOI: 10.1021/acs.jpcb.0c11633] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
4
Hayes BH, Tsai RK, Dooling LJ, Kadu S, Lee JY, Pantano D, Rodriguez PL, Subramanian S, Shin JW, Discher DE. Macrophages show higher levels of engulfment after disruption of cis interactions between CD47 and the checkpoint receptor SIRPα. J Cell Sci 2020;133:jcs.237800. [PMID: 31964705 DOI: 10.1242/jcs.237800] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/20/2019] [Indexed: 12/14/2022]  Open
5
Sayılgan JF, Haliloğlu T, Gönen M. Protein dynamics analysis reveals that missense mutations in cancer‐related genes appear frequently on hinge‐neighboring residues. Proteins 2019;87:512-519. [DOI: 10.1002/prot.25673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/09/2019] [Accepted: 02/17/2019] [Indexed: 01/26/2023]
6
Loop dynamics behind the affinity of DARPins towards ERK2: Molecular dynamics simulations (MDs) and elastic network model (ENM). J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.10.157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
7
Mishra SK, Jernigan RL. Protein dynamic communities from elastic network models align closely to the communities defined by molecular dynamics. PLoS One 2018;13:e0199225. [PMID: 29924847 PMCID: PMC6010283 DOI: 10.1371/journal.pone.0199225] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/04/2018] [Indexed: 11/22/2022]  Open
8
Laszlo KJ, Bush MF. Effects of Charge State, Charge Distribution, and Structure on the Ion Mobility of Protein Ions in Helium Gas: Results from Trajectory Method Calculations. J Phys Chem A 2017;121:7768-7777. [PMID: 28910102 DOI: 10.1021/acs.jpca.7b08154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
9
Postic G, Ghouzam Y, Chebrek R, Gelly JC. An ambiguity principle for assigning protein structural domains. SCIENCE ADVANCES 2017;3:e1600552. [PMID: 28097215 PMCID: PMC5235333 DOI: 10.1126/sciadv.1600552] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 11/28/2016] [Indexed: 05/20/2023]
10
Xia K, Opron K, Wei GW. Multiscale Gaussian network model (mGNM) and multiscale anisotropic network model (mANM). J Chem Phys 2016;143:204106. [PMID: 26627949 DOI: 10.1063/1.4936132] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
11
Streinu I. Large scale rigidity-based flexibility analysis of biomolecules. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016;3:012005. [PMID: 26958583 PMCID: PMC4760970 DOI: 10.1063/1.4942414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/08/2016] [Indexed: 06/05/2023]
12
Su JG, Zhang X, Han XM, Zhao SX, Li CH. The Intrinsic Dynamics and Unfolding Process of an Antibody Fab Fragment Revealed by Elastic Network Model. Int J Mol Sci 2015;16:29720-31. [PMID: 26690429 PMCID: PMC4691140 DOI: 10.3390/ijms161226197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/03/2015] [Accepted: 12/07/2015] [Indexed: 01/29/2023]  Open
13
Ponzoni L, Polles G, Carnevale V, Micheletti C. SPECTRUS: A Dimensionality Reduction Approach for Identifying Dynamical Domains in Protein Complexes from Limited Structural Datasets. Structure 2015;23:1516-1525. [PMID: 26165596 DOI: 10.1016/j.str.2015.05.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/23/2015] [Accepted: 05/29/2015] [Indexed: 02/06/2023]
14
Wieninger SA, Ullmann GM. CoMoDo: Identifying Dynamic Protein Domains Based on Covariances of Motion. J Chem Theory Comput 2015;11:2841-54. [DOI: 10.1021/acs.jctc.5b00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
15
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]
16
Guo NL, Wan YW. Network-based identification of biomarkers coexpressed with multiple pathways. Cancer Inform 2014;13:37-47. [PMID: 25392692 PMCID: PMC4218687 DOI: 10.4137/cin.s14054] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/25/2014] [Accepted: 06/29/2014] [Indexed: 02/07/2023]  Open
17
Noid WG. Perspective: Coarse-grained models for biomolecular systems. J Chem Phys 2014;139:090901. [PMID: 24028092 DOI: 10.1063/1.4818908] [Citation(s) in RCA: 566] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
18
Seo S, Jang Y, Qian P, Liu WK, Choi JB, Lim BS, Kim MK. Efficient prediction of protein conformational pathways based on the hybrid elastic network model. J Mol Graph Model 2013;47:25-36. [PMID: 24296313 DOI: 10.1016/j.jmgm.2013.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 10/19/2013] [Accepted: 10/22/2013] [Indexed: 11/18/2022]
19
McCoy AJ, Nicholls RA, Schneider TR. SCEDS: protein fragments for molecular replacement in Phaser. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013;69:2216-25. [PMID: 24189233 PMCID: PMC3817695 DOI: 10.1107/s0907444913021811] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 08/05/2013] [Indexed: 11/30/2022]
20
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]
21
Hall BA, Armitage JP, Sansom MSP. Mechanism of bacterial signal transduction revealed by molecular dynamics of Tsr dimers and trimers of dimers in lipid vesicles. PLoS Comput Biol 2012;8:e1002685. [PMID: 23028283 PMCID: PMC3447960 DOI: 10.1371/journal.pcbi.1002685] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 07/22/2012] [Indexed: 02/02/2023]  Open
22
Gur M, Erman B. Quasi-harmonic fluctuations of two bound peptides. Proteins 2012;80:2769-79. [DOI: 10.1002/prot.24160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 07/27/2012] [Accepted: 08/06/2012] [Indexed: 11/10/2022]
23
Issack BB, Berjanskii M, Wishart DS, Stepanova M. Exploring the essential collective dynamics of interacting proteins: application to prion protein dimers. Proteins 2012;80:1847-65. [PMID: 22488640 DOI: 10.1002/prot.24082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2011] [Revised: 03/07/2012] [Accepted: 03/18/2012] [Indexed: 11/11/2022]
24
Demerdash ONA, Mitchell JC. Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis. Proteins 2012;80:1766-79. [PMID: 22434479 DOI: 10.1002/prot.24072] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/13/2012] [Accepted: 03/12/2012] [Indexed: 11/10/2022]
25
Dietzen M, Zotenko E, Hildebrandt A, Lengauer T. On the applicability of elastic network normal modes in small-molecule docking. J Chem Inf Model 2012;52:844-56. [PMID: 22320151 DOI: 10.1021/ci2004847] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
26
Vinculin motion modes analysis with elastic network model. Int J Mol Sci 2012;13:208-20. [PMID: 22312248 PMCID: PMC3269682 DOI: 10.3390/ijms13010208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 12/11/2011] [Accepted: 12/12/2011] [Indexed: 12/02/2022]  Open
27
Guo NL. Network Medicine: New Paradigm in the -Omics Era. ACTA ACUST UNITED AC 2011;1. [PMID: 24634802 DOI: 10.4172/2161-0940.1000e106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
28
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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
29
Fernández JD, Vico FJ. Automating the search of molecular motor templates by evolutionary methods. Biosystems 2011;106:82-93. [PMID: 21784125 DOI: 10.1016/j.biosystems.2011.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 06/30/2011] [Accepted: 07/06/2011] [Indexed: 01/10/2023]
30
Minimalist models for proteins: a comparative analysis. Q Rev Biophys 2010;43:333-71. [PMID: 20707940 DOI: 10.1017/s0033583510000132] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
31
Integrating ion mobility mass spectrometry with molecular modelling to determine the architecture of multiprotein complexes. PLoS One 2010;5:e12080. [PMID: 20711472 PMCID: PMC2919415 DOI: 10.1371/journal.pone.0012080] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 07/09/2010] [Indexed: 11/21/2022]  Open
32
Lin TL, Song G. Generalized spring tensor models for protein fluctuation dynamics and conformation changes. BMC STRUCTURAL BIOLOGY 2010;10 Suppl 1:S3. [PMID: 20487510 PMCID: PMC2873826 DOI: 10.1186/1472-6807-10-s1-s3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
33
Yesylevskyy SO. New technique of identifying the hierarchy of dynamic domains in proteins using a method of molecular dynamics simulations. ACTA ACUST UNITED AC 2010. [DOI: 10.7124/bc.000151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
34
Abyzov A, Bjornson R, Felipe M, Gerstein M. RigidFinder: a fast and sensitive method to detect rigid blocks in large macromolecular complexes. Proteins 2010;78:309-24. [PMID: 19705487 DOI: 10.1002/prot.22544] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
35
Shudler M, Niv MY. BlockMaster: partitioning protein kinase structures using normal-mode analysis. J Phys Chem A 2009;113:7528-34. [PMID: 19485335 DOI: 10.1021/jp900885w] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
36
Potestio R, Pontiggia F, Micheletti C. Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits. Biophys J 2009;96:4993-5002. [PMID: 19527659 DOI: 10.1016/j.bpj.2009.03.051] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 03/24/2009] [Accepted: 03/25/2009] [Indexed: 12/19/2022]  Open
37
Keating KS, Flores SC, Gerstein MB, Kuhn LA. StoneHinge: hinge prediction by network analysis of individual protein structures. Protein Sci 2009;18:359-71. [PMID: 19180449 DOI: 10.1002/pro.38] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
38
Flores SC, Keating KS, Painter J, Morcos F, Nguyen K, Merritt EA, Kuhn LA, Gerstein MB. HingeMaster: normal mode hinge prediction approach and integration of complementary predictors. Proteins 2009;73:299-319. [PMID: 18433058 DOI: 10.1002/prot.22060] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
39
Yesylevskyy SO, Kharkyanen VN. Fuzzy domains: new way of describing flexibility and interdependence of the protein domains. Proteins 2009;74:980-95. [PMID: 18767167 DOI: 10.1002/prot.22208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
40
Leherte L, Vercauteren DP. Collective motions of rigid fragments in protein structures from smoothed electron density distributions. J Comput Chem 2008;29:1472-89. [DOI: 10.1002/jcc.20908] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
41
Yesylevskyy SO, Kharkyanen VN, Demchenko AP. The blind search for the closed states of hinge-bending proteins. Proteins 2007;71:831-43. [DOI: 10.1002/prot.21743] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
42
Hall BA, Kaye SL, Pang A, Perera R, Biggin PC. Characterization of protein conformational states by normal-mode frequencies. J Am Chem Soc 2007;129:11394-401. [PMID: 17715919 DOI: 10.1021/ja071797y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
43
Zhou H, Xue B, Zhou Y. DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile. Protein Sci 2007;16:947-55. [PMID: 17456745 PMCID: PMC2206635 DOI: 10.1110/ps.062597307] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
44
FlexOracle: predicting flexible hinges by identification of stable domains. BMC Bioinformatics 2007;8:215. [PMID: 17587456 PMCID: PMC1933439 DOI: 10.1186/1471-2105-8-215] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Accepted: 06/22/2007] [Indexed: 11/28/2022]  Open
45
Yang L, Song G, Jernigan RL. How well can we understand large-scale protein motions using normal modes of elastic network models? Biophys J 2007;93:920-9. [PMID: 17483178 PMCID: PMC1913142 DOI: 10.1529/biophysj.106.095927] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
46
Kondrashov DA, Cui Q, Phillips GN. Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data. Biophys J 2006;91:2760-7. [PMID: 16891367 PMCID: PMC1578481 DOI: 10.1529/biophysj.106.085894] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
47
Yesylevskyy SO, Kharkyanen VN, Demchenko AP. The change of protein intradomain mobility on ligand binding: is it a commonly observed phenomenon? Biophys J 2006;91:3002-13. [PMID: 16877502 PMCID: PMC1578460 DOI: 10.1529/biophysj.106.087866] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
48
Adcock SA, McCammon JA. Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev 2006;106:1589-615. [PMID: 16683746 PMCID: PMC2547409 DOI: 10.1021/cr040426m] [Citation(s) in RCA: 797] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
49
Yesylevskyy SO, Kharkyanen VN, Demchenko AP. Dynamic protein domains: identification, interdependence, and stability. Biophys J 2006;91:670-85. [PMID: 16632509 PMCID: PMC1483087 DOI: 10.1529/biophysj.105.078584] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
50
Bahar I, Rader AJ. Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 2006;15:586-92. [PMID: 16143512 PMCID: PMC1482533 DOI: 10.1016/j.sbi.2005.08.007] [Citation(s) in RCA: 540] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2005] [Revised: 07/09/2005] [Accepted: 08/24/2005] [Indexed: 10/25/2022]
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