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Volumn 12, Issue , 2011, Pages

MAVENs: Motion analysis and visualization of elastic networks and structural ensembles

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL SPEED; CONFORMATIONAL CHANGE; CONFORMATIONAL ENSEMBLE; DIRECTIONAL CORRELATIONS; ELASTIC NETWORK MODELS; FUNCTIONAL MOTIONS; INTEGRATED APPROACH; MIXED RESOLUTIONS;

EID: 79959582444     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-264     Document Type: Article
Times cited : (37)

References (41)
  • 1
    • 0016610491 scopus 로고
    • Computer simulation of protein folding
    • 10.1038/253694a0, 1167625
    • Levitt M, Warshel A. Computer simulation of protein folding. Nature 1975, 253:694-698. 10.1038/253694a0, 1167625.
    • (1975) Nature , vol.253 , pp. 694-698
    • Levitt, M.1    Warshel, A.2
  • 2
    • 0017776823 scopus 로고
    • Dynamics of folded proteins
    • 10.1038/267585a0, 301613
    • McCammon JA, Gelin BR, Karplus M. Dynamics of folded proteins. Nature 1977, 267:585-590. 10.1038/267585a0, 301613.
    • (1977) Nature , vol.267 , pp. 585-590
    • McCammon, J.A.1    Gelin, B.R.2    Karplus, M.3
  • 3
    • 27644502679 scopus 로고    scopus 로고
    • Simulating movement of tRNA into the ribosome during decoding
    • 10.1073/pnas.0503456102, 1266076, 16249344
    • Sanbonmatsu KY, Joseph S, Tung CS. Simulating movement of tRNA into the ribosome during decoding. Proc Natl Acad Sci USA 2005, 102:15854-15859. 10.1073/pnas.0503456102, 1266076, 16249344.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 15854-15859
    • Sanbonmatsu, K.Y.1    Joseph, S.2    Tung, C.S.3
  • 4
    • 0024712890 scopus 로고
    • Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA
    • 10.1016/S0006-3495(89)82676-1, 1280479, 2775828
    • Chou KC, Maggiora GM, Mao B. Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA. Biophys J 1989, 56:295-305. 10.1016/S0006-3495(89)82676-1, 1280479, 2775828.
    • (1989) Biophys J , vol.56 , pp. 295-305
    • Chou, K.C.1    Maggiora, G.M.2    Mao, B.3
  • 5
    • 0030940339 scopus 로고    scopus 로고
    • NMR evidence for slow collective motions in cyanometmyoglobin
    • 10.1038/nsb0497-292, 9095197
    • Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH. NMR evidence for slow collective motions in cyanometmyoglobin. Nat Struct Biol 1997, 4:292-297. 10.1038/nsb0497-292, 9095197.
    • (1997) Nat Struct Biol , vol.4 , pp. 292-297
    • Tolman, J.R.1    Flanagan, J.M.2    Kennedy, M.A.3    Prestegard, J.H.4
  • 6
    • 33746098487 scopus 로고    scopus 로고
    • Soliton/exciton transport in proteins
    • Sinkala Z. Soliton/exciton transport in proteins. J Theor Biol 2006, 241:919-927.
    • (2006) J Theor Biol , vol.241 , pp. 919-927
    • Sinkala, Z.1
  • 7
    • 77950392888 scopus 로고    scopus 로고
    • Anisotropic collective motion contributes to nuclear spin relaxation in crystalline proteins
    • 10.1021/ja907067j, 19916496
    • Lewandowski JR, Sein J, Blackledge M, Emsley L. Anisotropic collective motion contributes to nuclear spin relaxation in crystalline proteins. J Am Chem Soc 2010, 132:1246-1248. 10.1021/ja907067j, 19916496.
    • (2010) J Am Chem Soc , vol.132 , pp. 1246-1248
    • Lewandowski, J.R.1    Sein, J.2    Blackledge, M.3    Emsley, L.4
  • 8
    • 25444532318 scopus 로고    scopus 로고
    • Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings
    • 10.1073/pnas.0505129102, 1236556, 16172390
    • Bouvignies G, Bernado P, Meier S, Cho K, Grzesiek S, Bruschweiler R, Blackledge M. Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings. Proc Natl Acad Sci USA 2005, 102:13885-13890. 10.1073/pnas.0505129102, 1236556, 16172390.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 13885-13890
    • Bouvignies, G.1    Bernado, P.2    Meier, S.3    Cho, K.4    Grzesiek, S.5    Bruschweiler, R.6    Blackledge, M.7
  • 10
    • 38949218425 scopus 로고    scopus 로고
    • Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes
    • 10.1016/j.str.2007.12.011, 2350220, 18275822
    • Yang L, Song G, Carriquiry A, Jernigan RL. Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes. Structure 2008, 16:321-330. 10.1016/j.str.2007.12.011, 2350220, 18275822.
    • (2008) Structure , vol.16 , pp. 321-330
    • Yang, L.1    Song, G.2    Carriquiry, A.3    Jernigan, R.L.4
  • 11
    • 84872980168 scopus 로고    scopus 로고
    • Computational generation inhibitor-bound conformers of p38 map kinase and comparison with experiments
    • Bakan A, Bahar I. Computational generation inhibitor-bound conformers of p38 map kinase and comparison with experiments. Pac Symp Biocomput 2011, 181-192.
    • (2011) Pac Symp Biocomput , pp. 181-192
    • Bakan, A.1    Bahar, I.2
  • 12
    • 33748189629 scopus 로고    scopus 로고
    • The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models
    • 10.1021/ct600060d, 1948848, 17710199
    • 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. 10.1021/ct600060d, 1948848, 17710199.
    • (2006) J Chem Theory Comput , vol.2 , pp. 696-704
    • Sen, T.Z.1    Feng, Y.2    Garcia, J.V.3    Kloczkowski, A.4    Jernigan, R.L.5
  • 13
    • 34547666968 scopus 로고    scopus 로고
    • How well can we understand large-scale protein motions using normal modes of elastic network models?
    • 10.1529/biophysj.106.095927, 1913142, 17483178
    • 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, 93:920-929. 10.1529/biophysj.106.095927, 1913142, 17483178.
    • (2007) Biophys J , vol.93 , pp. 920-929
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 14
    • 39049185694 scopus 로고    scopus 로고
    • Packing regularities in biological structures relate to their dynamics
    • 2039702, 16957327
    • Jernigan RL, Kloczkowski A. Packing regularities in biological structures relate to their dynamics. Methods Mol Biol 2007, 350:251-276. 2039702, 16957327.
    • (2007) Methods Mol Biol , vol.350 , pp. 251-276
    • Jernigan, R.L.1    Kloczkowski, A.2
  • 15
    • 25844525600 scopus 로고    scopus 로고
    • The role of shape in determining molecular motions
    • 10.1529/biophysj.105.065904, 1366739, 16055547
    • Lu M, Ma J. The role of shape in determining molecular motions. Biophys J 2005, 89:2395-2401. 10.1529/biophysj.105.065904, 1366739, 16055547.
    • (2005) Biophys J , vol.89 , pp. 2395-2401
    • Lu, M.1    Ma, J.2
  • 16
    • 51149216498 scopus 로고
    • Analysis of Contribution of Internal Vibrations to Statistical Weights of Equilibrium Conformations of Macromolecules
    • Go N, Scheraga HA. Analysis of Contribution of Internal Vibrations to Statistical Weights of Equilibrium Conformations of Macromolecules. Journal of Chemical Physics 1969, 51, pg 4751-4767.e
    • (1969) Journal of Chemical Physics , vol.51 , pp. 4751-4767
    • Go, N.1    Scheraga, H.A.2
  • 17
    • 0020771265 scopus 로고
    • Dynamics of a small globular protein in terms of low-frequency vibrational modes
    • 10.1073/pnas.80.12.3696, 394117, 6574507
    • Go N, Noguti T, Nishikawa T. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc Natl Acad Sci USA 1983, 80:3696-3700. 10.1073/pnas.80.12.3696, 394117, 6574507.
    • (1983) Proc Natl Acad Sci USA , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 19
    • 58849116413 scopus 로고    scopus 로고
    • Application of elastic network models to proteins in the crystalline state
    • 10.1016/j.bpj.2008.10.010, 2716453, 19167297
    • Riccardi D, Cui Q, Phillips GN. Application of elastic network models to proteins in the crystalline state. Biophys J 2009, 96:464-475. 10.1016/j.bpj.2008.10.010, 2716453, 19167297.
    • (2009) Biophys J , vol.96 , pp. 464-475
    • Riccardi, D.1    Cui, Q.2    Phillips, G.N.3
  • 20
    • 68149141470 scopus 로고    scopus 로고
    • Protein elastic network models and the ranges of cooperativity
    • 10.1073/pnas.0902159106, 2718344, 19617554
    • Yang L, Song G, Jernigan RL. Protein elastic network models and the ranges of cooperativity. Proc Natl Acad Sci USA 2009, 106:12347-12352. 10.1073/pnas.0902159106, 2718344, 19617554.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 12347-12352
    • Yang, L.1    Song, G.2    Jernigan, R.L.3
  • 21
    • 77952586627 scopus 로고    scopus 로고
    • Generalized spring tensor models for protein fluctuation dynamics and conformation changes
    • 10.1186/1472-6807-10-S1-S3, 2873826, 20487510
    • Lin TL, Song G. Generalized spring tensor models for protein fluctuation dynamics and conformation changes. BMC Struct Biol 2010, 10(Suppl 1):S3. 10.1186/1472-6807-10-S1-S3, 2873826, 20487510.
    • (2010) BMC Struct Biol , vol.10 , Issue.SUPPL. 1
    • Lin, T.L.1    Song, G.2
  • 22
    • 77953147201 scopus 로고    scopus 로고
    • Torsional network model: normal modes in torsion angle space better correlate with conformation changes in proteins
    • Mendez R, Bastolla U. Torsional network model: normal modes in torsion angle space better correlate with conformation changes in proteins. Phys Rev Lett 2010, 104:228103.
    • (2010) Phys Rev Lett , vol.104 , pp. 228103
    • Mendez, R.1    Bastolla, U.2
  • 23
    • 69249187438 scopus 로고    scopus 로고
    • Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion
    • 10.1063/1.3167410, 2748695, 19708737
    • Stember JN, Wriggers W. Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion. J Chem Phys 2009, 131:074112. 10.1063/1.3167410, 2748695, 19708737.
    • (2009) J Chem Phys , vol.131 , pp. 074112
    • Stember, J.N.1    Wriggers, W.2
  • 24
    • 0037079578 scopus 로고    scopus 로고
    • Dynamics of large proteins through hierarchical levels of coarse-grained structures
    • 10.1002/jcc.1160, 11913377
    • Doruker P, Jernigan RL, Bahar I. Dynamics of large proteins through hierarchical levels of coarse-grained structures. J Comput Chem 2002, 23:119-127. 10.1002/jcc.1160, 11913377.
    • (2002) J Comput Chem , vol.23 , pp. 119-127
    • Doruker, P.1    Jernigan, R.L.2    Bahar, I.3
  • 25
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • 10.1016/S1359-0278(97)00024-2, 9218955
    • Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997, 2:173-181. 10.1016/S1359-0278(97)00024-2, 9218955.
    • (1997) Fold Des , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 27
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • 10.1103/PhysRevLett.77.1905, 10063201
    • Tirion MM. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Physical Review Letters 1996, 77:1905-1908. 10.1103/PhysRevLett.77.1905, 10063201.
    • (1996) Physical Review Letters , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 28
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • 10.1016/S0006-3495(01)76033-X, 1301252, 11159421
    • Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 2001, 80:505-515. 10.1016/S0006-3495(01)76033-X, 1301252, 11159421.
    • (2001) Biophys J , vol.80 , pp. 505-515
    • Atilgan, A.R.1    Durell, S.R.2    Jernigan, R.L.3    Demirel, M.C.4    Keskin, O.5    Bahar, I.6
  • 29
    • 0347753596 scopus 로고    scopus 로고
    • Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions
    • Kurkcuoglu O, Jernigan RL, Doruker P. Mixed levels of coarse-graining of large proteins using elastic network model succeeds in extracting the slowest motions. Polymer 2004, 45:649-657.
    • (2004) Polymer , vol.45 , pp. 649-657
    • Kurkcuoglu, O.1    Jernigan, R.L.2    Doruker, P.3
  • 30
    • 69449103989 scopus 로고    scopus 로고
    • Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model
    • 10.1016/j.bpj.2009.06.009, 2726304, 19686666
    • 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, 97:1178-1187. 10.1016/j.bpj.2009.06.009, 2726304, 19686666.
    • (2009) Biophys J , vol.97 , pp. 1178-1187
    • Kurkcuoglu, O.1    Turgut, O.T.2    Cansu, S.3    Jernigan, R.L.4    Doruker, P.5
  • 31
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • 10.1093/protein/14.1.1, 11287673
    • Tama F, Sanejouand YH. Conformational change of proteins arising from normal mode calculations. Protein Eng 2001, 14:1-6. 10.1093/protein/14.1.1, 11287673.
    • (2001) Protein Eng , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 32
    • 14844314722 scopus 로고    scopus 로고
    • An analysis of core deformations in protein superfamilies
    • 10.1529/biophysj.104.052449, 1305131, 15542556
    • Leo-Macias A, Lopez-Romero P, Lupyan D, Zerbino D, Ortiz AR. An analysis of core deformations in protein superfamilies. Biophys J 2005, 88:1291-1299. 10.1529/biophysj.104.052449, 1305131, 15542556.
    • (2005) Biophys J , vol.88 , pp. 1291-1299
    • Leo-Macias, A.1    Lopez-Romero, P.2    Lupyan, D.3    Zerbino, D.4    Ortiz, A.R.5
  • 33
    • 0141815545 scopus 로고    scopus 로고
    • Functional motions can be extracted from on-lattice construction of protein structures
    • 10.1002/prot.10486, 14517969
    • Doruker P, Jernigan RL. Functional motions can be extracted from on-lattice construction of protein structures. Proteins 2003, 53:174-181. 10.1002/prot.10486, 14517969.
    • (2003) Proteins , vol.53 , pp. 174-181
    • Doruker, P.1    Jernigan, R.L.2
  • 34
    • 33750407288 scopus 로고    scopus 로고
    • Anisotropic network model: systematic evaluation and a new web interface
    • 10.1093/bioinformatics/btl448, 16928735
    • Eyal E, Yang LW, Bahar I. Anisotropic network model: systematic evaluation and a new web interface. Bioinformatics 2006, 22:2619-2627. 10.1093/bioinformatics/btl448, 16928735.
    • (2006) Bioinformatics , vol.22 , pp. 2619-2627
    • Eyal, E.1    Yang, L.W.2    Bahar, I.3
  • 35
    • 3242875210 scopus 로고    scopus 로고
    • ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
    • 10.1093/nar/gkh368, 441506, 15215461
    • Suhre K, Sanejouand YH. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 2004, 32:W610-W614. 10.1093/nar/gkh368, 441506, 15215461.
    • (2004) Nucleic Acids Res , vol.32
    • Suhre, K.1    Sanejouand, Y.H.2
  • 36
    • 0345687171 scopus 로고    scopus 로고
    • A comparative study of motor-protein motions by using a simple elastic-network model
    • 10.1073/pnas.2235686100, 263771, 14585932
    • Zheng W, Doniach S. A comparative study of motor-protein motions by using a simple elastic-network model. Proc Natl Acad Sci USA 2003, 100:13253-13258. 10.1073/pnas.2235686100, 263771, 14585932.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 13253-13258
    • Zheng, W.1    Doniach, S.2
  • 37
    • 33747858757 scopus 로고    scopus 로고
    • NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis
    • 10.1093/nar/gkl082, 1538881, 16845062
    • Lindahl E, Azuara C, Koehl P, Delarue M. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res 2006, 34:W52-W56. 10.1093/nar/gkl082, 1538881, 16845062.
    • (2006) Nucleic Acids Res , vol.34
    • Lindahl, E.1    Azuara, C.2    Koehl, P.3    Delarue, M.4
  • 38
    • 34547586177 scopus 로고    scopus 로고
    • MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape
    • 10.1093/nar/gkm342, 1933200, 17545201
    • Franklin J, Koehl P, Doniach S, Delarue M. MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape. Nucleic Acids Res 2007, 35:W477-W482. 10.1093/nar/gkm342, 1933200, 17545201.
    • (2007) Nucleic Acids Res , vol.35
    • Franklin, J.1    Koehl, P.2    Doniach, S.3    Delarue, M.4
  • 39
    • 34848882812 scopus 로고    scopus 로고
    • Signal propagation in proteins and relation to equilibrium fluctuations
    • 1988854, 17892319
    • Chennubhotla C, Bahar I. Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput Biol 2007, 3:1716-1726. 1988854, 17892319.
    • (2007) PLoS Comput Biol , vol.3 , pp. 1716-1726
    • Chennubhotla, C.1    Bahar, I.2
  • 40
    • 0003845223 scopus 로고    scopus 로고
    • The PyMOL Molecular Graphics System
    • Schrödinger, LLC
    • The PyMOL Molecular Graphics System. 2011, 1.3. Schrödinger, LLC.
    • (2011) , vol.1-3
  • 41
    • 0029878720 scopus 로고    scopus 로고
    • VMD: visual molecular dynamics
    • 10.1016/0263-7855(96)00018-5, 8744570
    • Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996, 14:33-38. 10.1016/0263-7855(96)00018-5, 8744570.
    • (1996) J Mol Graph , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3


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