메뉴 건너뛰기




Volumn 28, Issue 19, 2012, Pages 2431-2440

Measuring and comparing structural fluctuation patterns in large protein datasets

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 84867313359     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts445     Document Type: Article
Times cited : (111)

References (38)
  • 1
    • 78349254189 scopus 로고    scopus 로고
    • Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses
    • Ahmed,A. et al. (2010) Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses. Proteins, 78, 3341-3352.
    • (2010) Proteins , vol.78 , pp. 3341-3352
    • Ahmed, A.1
  • 2
    • 0032802062 scopus 로고    scopus 로고
    • On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations
    • Amadei,A. et al. (1999) On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. Proteins, 36, 419-424.
    • (1999) Proteins , vol.36 , pp. 419-424
    • Amadei, A.1
  • 3
    • 77952938726 scopus 로고    scopus 로고
    • Global dynamics of proteins: bridging between structure and function
    • Bahar,I. et al. (2010) Global dynamics of proteins: bridging between structure and function. Ann. Rev. Biophys., 39, 23-42.
    • (2010) Ann. Rev. Biophys. , vol.39 , pp. 23-42
    • Bahar, I.1
  • 4
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 5
    • 0000585273 scopus 로고
    • On a measure of divergence between two multinomial populations
    • Bhattacharyya,A. (1943) On a measure of divergence between two multinomial populations. Sankhya: Indian J. Statist., 7, 401-406.
    • (1943) Sankhya: Indian J. Statist. , vol.7 , pp. 401-406
    • Bhattacharyya, A.1
  • 6
    • 33746651090 scopus 로고    scopus 로고
    • Convergent dynamics in the protease enzymatic superfamily
    • Carnevale,V. et al. (2006) Convergent dynamics in the protease enzymatic superfamily. J. Am. Chem. Soc., 128, 9766-9772.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 9766-9772
    • Carnevale, V.1
  • 7
    • 34547702378 scopus 로고    scopus 로고
    • Structural and dynamical alignment of enzymes with partial structural similarity
    • SISSA, CNR, INFM Democritos, I-34014 Trieste, Italy
    • Carnevale,V. et al. (2007) Structural and dynamical alignment of enzymes with partial structural similarity. In Journal of Physics-Condensed Matter, SISSA, CNR, INFM Democritos, I-34014 Trieste, Italy.
    • (2007) Journal of Physics-Condensed Matter
    • Carnevale, V.1
  • 8
    • 0348129526 scopus 로고    scopus 로고
    • The ASTRAL Compendium in 2004
    • Chandonia,J.-M. et al. (2004) The ASTRAL Compendium in 2004. Nucleic Acids Res., 32, D189-D192.
    • (2004) Nucleic Acids Res , vol.32
    • Chandonia, J.-M.1
  • 9
    • 77949400204 scopus 로고    scopus 로고
    • A perturbative view of protein structural variation
    • Echave,J. and Fernández,F.M. (2010) A perturbative view of protein structural variation. Proteins, 78, 173-180.
    • (2010) Proteins , vol.78 , pp. 173-180
    • Echave, J.1    Fernández, F.M.2
  • 10
    • 0001969211 scopus 로고    scopus 로고
    • Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching
    • Gribskov,M. and Robinson,N.L. (1996) Use of receiver operating characteristic (ROC) analysis to evaluate sequence matching. Comput. Chem., 20, 25-33.
    • (1996) Comput. Chem. , vol.20 , pp. 25-33
    • Gribskov, M.1    Robinson, N.L.2
  • 11
    • 0020083498 scopus 로고
    • The meaning and use of the area under a receiver operating characteristic (ROC) curve
    • Hanley,J.A. and McNeil,B.J. (1982) The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology, 143, 29-36.
    • (1982) Radiology , vol.143 , pp. 29-36
    • Hanley, J.A.1    McNeil, B.J.2
  • 12
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • Henzler-Wildman,K. and Kern,D. (2007) Dynamic personalities of proteins. Nature, 450, 964-972.
    • (2007) Nature , vol.450 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 13
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen,K. (1998) Analysis of domain motions by approximate normal mode calculations. Proteins, 33, 417-429.
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 14
    • 0034333103 scopus 로고    scopus 로고
    • Harmonicity in slow protein dynamics
    • Hinsen,K. et al. (2000) Harmonicity in slow protein dynamics. Chem. Phys., 261, 25-37.
    • (2000) Chem. Phys. , vol.261 , pp. 25-37
    • Hinsen, K.1
  • 15
    • 78650768719 scopus 로고    scopus 로고
    • Exploring the factors determining the dynamics of different protein folds
    • Hollup,S.M. et al. (2011) Exploring the factors determining the dynamics of different protein folds. Protein Science, 20, 197-209.
    • (2011) Protein Science , vol.20 , pp. 197-209
    • Hollup, S.M.1
  • 16
    • 0034029144 scopus 로고    scopus 로고
    • Proteins with similar architecture exhibit similar large-scale dynamic behavior
    • Keskin,O. et al. (2000) Proteins with similar architecture exhibit similar large-scale dynamic behavior. Biophys. J., 78, 2093-2106.
    • (2000) Biophys. J. , vol.78 , pp. 2093-2106
    • Keskin, O.1
  • 17
    • 14844314722 scopus 로고    scopus 로고
    • An analysis of core deformations in protein superfamilies
    • Leo-Macias,A. et al. (2005) An analysis of core deformations in protein superfamilies. Biophys. J., 88, 1291-1299.
    • (2005) Biophys. J. , vol.88 , pp. 1291-1299
    • Leo-Macias, A.1
  • 18
    • 0036084625 scopus 로고    scopus 로고
    • SCOP database in 2002 refinements accommodate structural genomics
    • Lo Conte,L. et al. (2002) SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res., 30, 264-267.
    • (2002) Nucleic Acids Res , vol.30 , pp. 264-267
    • Lo Conte, L.1
  • 19
    • 23244450294 scopus 로고    scopus 로고
    • Exploring the common dynamics of homologous proteins Application to the globin family
    • Maguid,S. et al. (2005) Exploring the common dynamics of homologous proteins. Application to the globin family. Biophys. J., 89, 3-13.
    • (2005) Biophys. J. , vol.89 , pp. 3-13
    • Maguid, S.1
  • 20
    • 33750228192 scopus 로고    scopus 로고
    • Evolutionary conservation of protein backbone flexibility
    • Maguid,S. et al. (2006) Evolutionary conservation of protein backbone flexibility. J. Mol. Evol., 63, 448-457.
    • (2006) J. Mol. Evol. , vol.63 , pp. 448-457
    • Maguid, S.1
  • 21
    • 49049096095 scopus 로고    scopus 로고
    • Evolutionary conservation of protein vibrational dynamics
    • Maguid,S. et al. (2008) Evolutionary conservation of protein vibrational dynamics. Gene, 422, 7-13.
    • (2008) Gene , vol.422 , pp. 7-13
    • Maguid, S.1
  • 22
    • 0002322469 scopus 로고
    • On a test of whether one of two random variables is stochastically larger than the other
    • Mann, H.B. and Whitney,D.R. (1947) On a test of whether one of two random variables is stochastically larger than the other. Ann. Math. Statis., 18, 50-60.
    • (1947) Ann. Math. Statis. , vol.18 , pp. 50-60
    • Mann, H.B.1    Whitney, D.R.2
  • 23
    • 80053440006 scopus 로고    scopus 로고
    • Binding leverage as a molecular basis for allosteric regulation
    • Mitternacht,S. and Berezovsky,I.N. (2011a) Binding leverage as a molecular basis for allosteric regulation. PLoS Comput. Biol., 7, e1002148.
    • (2011) PLoS Comput. Biol. , vol.7
    • Mitternacht, S.1    Berezovsky, I.N.2
  • 24
    • 84855283469 scopus 로고    scopus 로고
    • Coherent conformational degrees of freedom as a structural basis for allosteric communication
    • Mitternacht,S. and Berezovsky,I.N. (2011b) Coherent conformational degrees of freedom as a structural basis for allosteric communication. PLoS Comput. Biol., 7, e1002301.
    • (2011) PLoS Comput. Biol. , vol.7
    • Mitternacht, S.1    Berezovsky, I.N.2
  • 25
    • 77950667485 scopus 로고    scopus 로고
    • Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity
    • Münz,M. et al. (2010) Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity. BMC Bioinformatics, 11, 188.
    • (2010) BMC Bioinformatics , vol.11 , pp. 188
    • Münz, M.1
  • 26
    • 0028961335 scopus 로고
    • SCOP-a structural classification of proteins Database for the investigation of sequences and structures
    • Murzin,A.G. et al. (1995) SCOP-a structural classification of proteins. Database for the investigation of sequences and structures. J. Mole. Biol., 247, 536-540.
    • (1995) J. Mole. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1
  • 27
    • 34547728641 scopus 로고    scopus 로고
    • Detecting similarities among distant homologous proteins by comparison of domain flexibilities
    • Pandini,A. et al. (2007) Detecting similarities among distant homologous proteins by comparison of domain flexibilities. Prot. Eng. Design Select., 20, 285-299.
    • (2007) Prot. Eng. Design Select. , vol.20 , pp. 285-299
    • Pandini, A.1
  • 28
    • 28644451763 scopus 로고    scopus 로고
    • Comparative molecular dynamics-similar folds and similar motions?
    • Pang,A. et al. (2005) Comparative molecular dynamics-similar folds and similar motions? Proteins, 61, 809-822.
    • (2005) Proteins , vol.61 , pp. 809-822
    • Pang, A.1
  • 29
    • 33747756504 scopus 로고    scopus 로고
    • Flexibility and enzymatic cold-adaptation: a comparative molecular dynamics investigation of the elastase family
    • Papaleo,E. et al. (2006) Flexibility and enzymatic cold-adaptation: a comparative molecular dynamics investigation of the elastase family. BBA-Prot. Proteom., 1764, 1397-1406.
    • (2006) BBA-Prot. Proteom. , vol.1764 , pp. 1397-1406
    • Papaleo, E.1
  • 30
    • 77954286692 scopus 로고    scopus 로고
    • ALADYN: a web server for aligning proteins by matching their large-scale motion
    • Potestio,R. et al. (2010) ALADYN: a web server for aligning proteins by matching their large-scale motion. Nucleic Acids Res., 38(Web Server), W41-W45.
    • (2010) Nucleic Acids Res , vol.38 , Issue.WEB SERVER
    • Potestio, R.1
  • 31
    • 77649134951 scopus 로고    scopus 로고
    • Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily
    • Raimondi,F. et al. (2010) Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily. Structure, 18, 402-414.
    • (2010) Structure , vol.18 , pp. 402-414
    • Raimondi, F.1
  • 32
    • 34248159870 scopus 로고    scopus 로고
    • Thorough validation of protein normal mode analysis: a comparative study with essential dynamics
    • Rueda,M. et al. (2007) Thorough validation of protein normal mode analysis: a comparative study with essential dynamics. Structure, 15, 565-575.
    • (2007) Structure , vol.15 , pp. 565-575
    • Rueda, M.1
  • 33
    • 0026743174 scopus 로고
    • Multiple protein-sequence alignment from tertiary structure comparison-assignment of global and residue confidence levels
    • Russell,R. and Barton,G. (1992) Multiple protein-sequence alignment from tertiary structure comparison-assignment of global and residue confidence levels. Proteins, 14, 309-323.
    • (1992) Proteins , vol.14 , pp. 309-323
    • Russell, R.1    Barton, G.2
  • 34
    • 78649784550 scopus 로고    scopus 로고
    • Principal component and normal mode analysis of proteins; a quantitative comparison using theGroEL subunit
    • Skjaerven,L. et al. (2011) Principal component and normal mode analysis of proteins; a quantitative comparison using theGroEL subunit. Proteins, 79, 232-243.
    • (2011) Proteins , vol.79 , pp. 232-243
    • Skjaerven, L.1
  • 35
    • 43149103140 scopus 로고    scopus 로고
    • ROC analysis: applications to the classification of biological sequences and 3D structures
    • Sonego,P. et al. (2008) ROC analysis: applications to the classification of biological sequences and 3D structures. Brief. Bioinformatics, 9, 198-209.
    • (2008) Brief. Bioinformatics , vol.9 , pp. 198-209
    • Sonego, P.1
  • 36
    • 38949218425 scopus 로고    scopus 로고
    • Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes
    • Yang,L. et al. (2008) Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes. Structure, 16, 321-330.
    • (2008) Structure , vol.16 , pp. 321-330
    • Yang, L.1
  • 37
    • 43049104657 scopus 로고    scopus 로고
    • Correspondences between low-energy modes in enzymes: Dynamics-basedalignmentof enzymatic functional families
    • Zen,A. et al. (2008) Correspondences between low-energy modes in enzymes: Dynamics-basedalignmentof enzymatic functional families.Prot.Sci.,17,918-929.
    • (2008) Prot. Sci. , vol.17 , pp. 918-929
    • Zen, A.1
  • 38
    • 67650745346 scopus 로고    scopus 로고
    • Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains
    • Zen,A. et al. (2009) Using dynamics-based comparisons to predict nucleic acid binding sites in proteins: an application to OB-fold domains. Bioinformatics, 25, 1876-1883.
    • (2009) Bioinformatics , vol.25 , pp. 1876-1883
    • Zen, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.