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For: Ma J. New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr Protein Pept Sci 2004;5:119-23. [PMID: 15078222 PMCID: PMC2688808 DOI: 10.2174/1389203043486892] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Number Cited by Other Article(s)
1
Sankar K, Mishra SK, Jernigan RL. Comparisons of Protein Dynamics from Experimental Structure Ensembles, Molecular Dynamics Ensembles, and Coarse-Grained Elastic Network Models. J Phys Chem B 2018;122:5409-5417. [DOI: 10.1021/acs.jpcb.7b11668] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
2
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: 0.9] [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]
3
Peptide Inhibitors Targeting the Neisseria gonorrhoeae Pivotal Anaerobic Respiration Factor AniA. Antimicrob Agents Chemother 2017;61:AAC.00186-17. [PMID: 28584144 DOI: 10.1128/aac.00186-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 05/27/2017] [Indexed: 12/24/2022]  Open
4
Na H, Song G, ben-Avraham D. Universality of vibrational spectra of globular proteins. Phys Biol 2016;13:016008. [DOI: 10.1088/1478-3975/13/1/016008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
5
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: 0.7] [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
6
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] [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
7
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: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
8
Study of protein structural deformations under external mechanical perturbations by a coarse-grained simulation method. Biomech Model Mechanobiol 2015;15:317-29. [DOI: 10.1007/s10237-015-0690-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/30/2015] [Indexed: 01/14/2023]
9
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: 1.4] [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]
10
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: 2.1] [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]
11
Stambouli N, Dridi M, Wei NN, Jlizi A, Bouraoui A, Elgaaied ABA. Structural insight into the binding complex: β-arrestin/CCR5 complex. J Biomol Struct Dyn 2013;32:866-75. [PMID: 24404772 DOI: 10.1080/07391102.2013.794373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
12
Localized lipid packing of transmembrane domains impedes integrin clustering. PLoS Comput Biol 2013;9:e1002948. [PMID: 23516344 PMCID: PMC3597534 DOI: 10.1371/journal.pcbi.1002948] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 01/11/2013] [Indexed: 12/12/2022]  Open
13
PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment. J Mol Biol 2013;425:1082-98. [PMID: 23333742 DOI: 10.1016/j.jmb.2012.12.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 12/31/2012] [Indexed: 11/21/2022]
14
Wei NN, Hamza A, Hao C, Johnson-Scalise T, Xiu Z, Naftolin F, Zhan CG. Protein flexibility and conformational states of Leishmania antigen eIF-4A: identification of a novel plausible protein adjuvant using comparative genomics and molecular modeling. J Biomol Struct Dyn 2012;31:841-53. [PMID: 22963753 DOI: 10.1080/07391102.2012.713781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
15
Jiang W, Ghosh D. Motion and flexibility in human cytochrome p450 aromatase. PLoS One 2012;7:e32565. [PMID: 22384274 PMCID: PMC3288111 DOI: 10.1371/journal.pone.0032565] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Accepted: 01/31/2012] [Indexed: 11/26/2022]  Open
16
Wang B, Weng J, Fan K, Wang W. Elastic network model-based normal mode analysis reveals the conformational couplings in the tripartite AcrAB-TolC multidrug efflux complex. Proteins 2011;79:2936-45. [PMID: 21905116 DOI: 10.1002/prot.23143] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 06/20/2011] [Accepted: 07/20/2011] [Indexed: 11/08/2022]
17
Tran HT, Zhang S. Accurate prediction of the bound form of the Akt pleckstrin homology domain using normal mode analysis to explore structural flexibility. J Chem Inf Model 2011;51:2352-60. [PMID: 21834588 DOI: 10.1021/ci2001742] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
18
Liu L, Liu X, Gong J, Jiang H, Li H. Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit. J Chem Theory Comput 2011;7:1595-603. [DOI: 10.1021/ct100728k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
19
Ahmed A, Villinger S, Gohlke H. Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses. Proteins 2011;78:3341-52. [PMID: 20848551 DOI: 10.1002/prot.22841] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
20
A molecular dynamics investigation of vinculin activation. Biophys J 2010;99:1073-81. [PMID: 20712990 DOI: 10.1016/j.bpj.2010.05.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 05/07/2010] [Accepted: 05/12/2010] [Indexed: 11/23/2022]  Open
21
Chirikjian GS. Group theory and biomolecular conformation: I. Mathematical and computational models. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010;22:323103. [PMID: 20827378 PMCID: PMC2935091 DOI: 10.1088/0953-8984/22/32/323103] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
22
Miloshevsky GV, Hassanein A, Jordan PC. Shape-Dependent Global Deformation Modes of Large Protein Structures. J Mol Struct 2010;972:41-50. [PMID: 20526444 PMCID: PMC2878971 DOI: 10.1016/j.molstruc.2010.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
23
Mashiach E, Nussinov R, Wolfson HJ. FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins 2010;78:1503-19. [PMID: 20077569 PMCID: PMC4290165 DOI: 10.1002/prot.22668] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
24
Liu LT, Haddadian EJ, Willenbring D, Xu Y, Tang P. Higher susceptibility to halothane modulation in open- than in closed-channel alpha4beta2 nAChR revealed by molecular dynamics simulations. J Phys Chem B 2010;114:626-32. [PMID: 20014754 DOI: 10.1021/jp908944e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
25
Moritsugu K, Njunda BM, Smith JC. Theory and Normal-Mode Analysis of Change in Protein Vibrational Dynamics on Ligand Binding. J Phys Chem B 2009;114:1479-85. [DOI: 10.1021/jp909677p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
26
Liu LT, Willenbring D, Xu Y, Tang P. General anesthetic binding to neuronal alpha4beta2 nicotinic acetylcholine receptor and its effects on global dynamics. J Phys Chem B 2009;113:12581-9. [PMID: 19697903 DOI: 10.1021/jp9039513] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
27
A Minimalist Network Model for Studying Biomolecular Vibration. Proteins 2009. [DOI: 10.1201/9781420087048-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
28
Coarse-grained modeling of allosteric regulation in protein receptors. Proc Natl Acad Sci U S A 2009;106:14253-8. [PMID: 19706508 DOI: 10.1073/pnas.0901811106] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
29
Golji J, Collins R, Mofrad MRK. Molecular mechanics of the alpha-actinin rod domain: bending, torsional, and extensional behavior. PLoS Comput Biol 2009;5:e1000389. [PMID: 19436721 PMCID: PMC2676514 DOI: 10.1371/journal.pcbi.1000389] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Accepted: 04/15/2009] [Indexed: 11/19/2022]  Open
30
Chen X, Lu M, Poon BK, Wang Q, Ma J. Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009;65:339-47. [PMID: 19307715 PMCID: PMC2659883 DOI: 10.1107/s0907444909003539] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Accepted: 01/28/2009] [Indexed: 11/10/2022]
31
Andrusier N, Mashiach E, Nussinov R, Wolfson HJ. Principles of flexible protein-protein docking. Proteins 2009;73:271-89. [PMID: 18655061 DOI: 10.1002/prot.22170] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
32
Kong Y, Karplus M. Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis. Proteins 2009;74:145-54. [PMID: 18618698 DOI: 10.1002/prot.22139] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
33
Chandran PL, Mofrad MRK. Rods-on-string idealization captures semiflexible filament dynamics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009;79:011906. [PMID: 19257068 DOI: 10.1103/physreve.79.011906] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Indexed: 05/27/2023]
34
A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography. Proc Natl Acad Sci U S A 2008;105:15358-63. [PMID: 18832168 DOI: 10.1073/pnas.0806072105] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
35
Wu Y, Tian X, Lu M, Chen M, Wang Q, Ma J. Folding of small helical proteins assisted by small-angle X-ray scattering profiles. Structure 2008;13:1587-97. [PMID: 16271882 DOI: 10.1016/j.str.2005.07.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Revised: 07/21/2005] [Accepted: 07/22/2005] [Indexed: 10/25/2022]
36
Chen X, Poon BK, Dousis A, Wang Q, Ma J. Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution. Structure 2007;15:955-62. [PMID: 17698000 PMCID: PMC3136661 DOI: 10.1016/j.str.2007.06.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 06/05/2007] [Accepted: 06/18/2007] [Indexed: 10/23/2022]
37
The conformational coupling and translocation mechanism of vitamin B12 ATP-binding cassette transporter BtuCD. Biophys J 2007;94:612-21. [PMID: 17951296 DOI: 10.1529/biophysj.107.110734] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
38
Szarecka A, Xu Y, Tang P. Dynamics of heteropentameric nicotinic acetylcholine receptor: implications of the gating mechanism. Proteins 2007;68:948-60. [PMID: 17546671 DOI: 10.1002/prot.21462] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
39
Poon BK, Chen X, Lu M, Vyas NK, Quiocho FA, Wang Q, Ma J. Normal mode refinement of anisotropic thermal parameters for a supramolecular complex at 3.42-A crystallographic resolution. Proc Natl Acad Sci U S A 2007;104:7869-74. [PMID: 17470791 PMCID: PMC1876539 DOI: 10.1073/pnas.0701204104] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2007] [Indexed: 11/18/2022]  Open
40
Schmidberger JW, Wilce JA, Tsang JSH, Wilce MCJ. Crystal structures of the substrate free-enzyme, and reaction intermediate of the HAD superfamily member, haloacid dehalogenase DehIVa from Burkholderia cepacia MBA4. J Mol Biol 2007;368:706-17. [PMID: 17368477 DOI: 10.1016/j.jmb.2007.02.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Revised: 02/02/2007] [Accepted: 02/07/2007] [Indexed: 11/17/2022]
41
Xing J, Kim KS. Protein fluctuations and breakdown of time-scale separation in rate theories. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006;74:061911. [PMID: 17280100 DOI: 10.1103/physreve.74.061911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Revised: 10/03/2006] [Indexed: 05/13/2023]
42
Gohlke H, Thorpe MF. A natural coarse graining for simulating large biomolecular motion. Biophys J 2006;91:2115-20. [PMID: 16815893 PMCID: PMC1557556 DOI: 10.1529/biophysj.106.083568] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
43
Lu M, Poon B, Ma J. A New Method for Coarse-Grained Elastic Normal-Mode Analysis. J Chem Theory Comput 2006;2:464-471. [PMID: 21760758 DOI: 10.1021/ct050307u] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
44
Best RB, Chen YG, Hummer G. Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor. Structure 2006;13:1755-63. [PMID: 16338404 DOI: 10.1016/j.str.2005.08.009] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2005] [Revised: 08/02/2005] [Accepted: 08/10/2005] [Indexed: 10/25/2022]
45
Kong Y, Ma J, Karplus M, Lipscomb WN. The Allosteric Mechanism of Yeast Chorismate Mutase: A Dynamic Analysis. J Mol Biol 2006;356:237-47. [PMID: 16337651 DOI: 10.1016/j.jmb.2005.10.064] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 10/20/2005] [Accepted: 10/23/2005] [Indexed: 11/16/2022]
46
Cui Q. Theoretical and computational studies of vectorial processes in biomolecular systems. Theor Chem Acc 2006. [DOI: 10.1007/s00214-005-0022-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
47
Xing J, Liao JC, Oster G. Making ATP. Proc Natl Acad Sci U S A 2005;102:16539-46. [PMID: 16217018 PMCID: PMC1283826 DOI: 10.1073/pnas.0507207102] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
48
Ma J. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 2005;13:373-80. [PMID: 15766538 DOI: 10.1016/j.str.2005.02.002] [Citation(s) in RCA: 369] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
49
Lu M, Ma J. The role of shape in determining molecular motions. Biophys J 2005;89:2395-401. [PMID: 16055547 PMCID: PMC1366739 DOI: 10.1529/biophysj.105.065904] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
50
Yang LW, Liu X, Jursa CJ, Holliman M, Rader AJ, Karimi HA, Bahar I. iGNM: a database of protein functional motions based on Gaussian Network Model. Bioinformatics 2005;21:2978-87. [PMID: 15860562 PMCID: PMC1752228 DOI: 10.1093/bioinformatics/bti469] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
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