메뉴 건너뛰기




Volumn 24, Issue 19, 2008, Pages 2184-2192

Mixture models for protein structure ensembles

Author keywords

[No Author keywords available]

Indexed keywords

CALMODULIN; GLOBULAR PROTEIN;

EID: 52949143542     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn396     Document Type: Article
Times cited : (10)

References (28)
  • 1
    • 35448929112 scopus 로고    scopus 로고
    • A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing
    • Andrec,M. et al. (2007) A large data set comparison of protein structures determined by crystallography and NMR: Statistical test for structural differences and the effect of crystal packing. Proteins Struct. Funct. Bioinform., 69, 449-465.
    • (2007) Proteins Struct. Funct. Bioinform , vol.69 , pp. 449-465
    • Andrec, M.1
  • 2
    • 0030816707 scopus 로고    scopus 로고
    • Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: Cytochrome P450BM-3
    • Arnold,G.E. and Omstein,R.L. (1997) Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3. Biophys. J., 73, 1147-1159.
    • (1997) Biophys. J , vol.73 , pp. 1147-1159
    • Arnold, G.E.1    Omstein, R.L.2
  • 4
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the EM algorithm (with discussion)
    • Dempster,A.P. et al. (1977) Maximum likelihood from incomplete data via the EM algorithm (with discussion). J. R. Stat. Soc. B, 39, 1-38.
    • (1977) J. R. Stat. Soc. B , vol.39 , pp. 1-38
    • Dempster, A.P.1
  • 5
    • 33644807131 scopus 로고    scopus 로고
    • Is one solution good enough?
    • Furnham,N. et al. (2006) Is one solution good enough? Nat. Struct. Biol., 13, 184-185.
    • (2006) Nat. Struct. Biol , vol.13 , pp. 184-185
    • Furnham, N.1
  • 6
    • 0028335096 scopus 로고
    • Structural mechanisms for domain movements in proteins
    • Gerstein,M. et al. (1994) Structural mechanisms for domain movements in proteins. Biochemistry, 33, 6739-6749.
    • (1994) Biochemistry , vol.33 , pp. 6739-6749
    • Gerstein, M.1
  • 7
    • 0022429234 scopus 로고
    • An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution
    • Havel,T.F. and Wüthrich,K. (1985) An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution. J. Mol. Biol., 182, 281-294.
    • (1985) J. Mol. Biol , vol.182 , pp. 281-294
    • Havel, T.F.1    Wüthrich, K.2
  • 8
    • 0001930482 scopus 로고
    • Matrix nearness problems and applications
    • Gover,M.J.C. and Barnett,S, eds, Oxford University Press, Oxford, UK, pp
    • Higham,N.J. (1989) Matrix nearness problems and applications. In Gover,M.J.C. and Barnett,S. (eds) Applications of Matrix Theory. Oxford University Press, Oxford, UK, pp. 1-27.
    • (1989) Applications of Matrix Theory , pp. 1-27
    • Higham, N.J.1
  • 9
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch,W. (1976) A solution for the best rotation to relate two sets of vectors. Acta Cryst., A32, 922-923.
    • (1976) Acta Cryst , vol.A32 , pp. 922-923
    • Kabsch, W.1
  • 10
    • 0029831680 scopus 로고    scopus 로고
    • An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
    • Kelley,L.A. et al. (1996) An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Protein Eng., 9, 1063-1065.
    • (1996) Protein Eng , vol.9 , pp. 1063-1065
    • Kelley, L.A.1
  • 11
    • 0030843113 scopus 로고    scopus 로고
    • An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures
    • Kelley,L.A. et al. (1997) An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures. Protein Eng., 10, 737-741.
    • (1997) Protein Eng , vol.10 , pp. 737-741
    • Kelley, L.A.1
  • 12
    • 0029159794 scopus 로고
    • Solution structure of calcium-free calmodulin
    • Kuboniwa,H. et al. (1995) Solution structure of calcium-free calmodulin. Nat. Struct. Biol., 2, 768-776.
    • (1995) Nat. Struct. Biol , vol.2 , pp. 768-776
    • Kuboniwa, H.1
  • 14
    • 0032584781 scopus 로고    scopus 로고
    • Recommendations for the presentation of NMR structures of proteins and nucleic acids
    • Markley,J.L. et al. (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids. J. Mol. Biol., 280, 933-952.
    • (1998) J. Mol. Biol , vol.280 , pp. 933-952
    • Markley, J.L.1
  • 15
    • 33646260450 scopus 로고    scopus 로고
    • Optimal description of a protein structure in terms of multiple groups undergoing TTS motion
    • Painter,J. and Merritt, E.A. (2006) Optimal description of a protein structure in terms of multiple groups undergoing TTS motion. Acta Crystallogr. D Biol. Crystallogr., 62, 439-450.
    • (2006) Acta Crystallogr. D Biol. Crystallogr , vol.62 , pp. 439-450
    • Painter, J.1    Merritt, E.A.2
  • 16
    • 79955803023 scopus 로고    scopus 로고
    • The infinite gaussian mixture model
    • Solla,S.A.T.K. and Müller,K.R, eds, MIT Press, Cambridge, MA, pp
    • Rasmussen,C.E. (2000) The infinite gaussian mixture model. In Solla,S.A.T.K. and Müller,K.R. (eds) NIPS 12. MIT Press, Cambridge, MA, pp. 554-560.
    • (2000) NIPS 12 , pp. 554-560
    • Rasmussen, C.E.1
  • 17
    • 22144489530 scopus 로고    scopus 로고
    • Inferential structure determination
    • Rieping,W. et al. (2005) Inferential structure determination. Science, 309, 303-306.
    • (2005) Science , vol.309 , pp. 303-306
    • Rieping, W.1
  • 18
    • 18844415920 scopus 로고    scopus 로고
    • Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles
    • Snyder,D.A. and Montelione,GT. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Proteins Struct. Funct. Bioinform. 59, 673-686.
    • (2005) Proteins Struct. Funct. Bioinform , vol.59 , pp. 673-686
    • Snyder, D.A.1    Montelione, G.T.2
  • 19
    • 18844433630 scopus 로고    scopus 로고
    • Assessing precision and accuracy of protein structures derived from NMR data
    • Snyder,D.A. et al. (2005) Assessing precision and accuracy of protein structures derived from NMR data. Proteins Struct. Funct. Bioinform. 59, 655-661.
    • (2005) Proteins Struct. Funct. Bioinform , vol.59 , pp. 655-661
    • Snyder, D.A.1
  • 20
    • 0037357143 scopus 로고    scopus 로고
    • The precision of NMR structure ensembles revisited
    • Spronk,A.E.M. et al. (2003) The precision of NMR structure ensembles revisited. J. Biomol. NMR, 25, 225-234.
    • (2003) J. Biomol. NMR , vol.25 , pp. 225-234
    • Spronk, A.E.M.1
  • 21
    • 0000629975 scopus 로고
    • Cross-validatory choice and assessment of statistical predictions
    • Stone,M. (1974) Cross-validatory choice and assessment of statistical predictions. J. R. Stat. Soc. B, 36, 111-147.
    • (1974) J. R. Stat. Soc. B , vol.36 , pp. 111-147
    • Stone, M.1
  • 22
    • 0027178211 scopus 로고
    • Representing an ensemble of NMR-derived protein structures by a single structure
    • Sutcliffe,M.J. (1993) Representing an ensemble of NMR-derived protein structures by a single structure. Protein Sci., 2, 936-944.
    • (1993) Protein Sci , vol.2 , pp. 936-944
    • Sutcliffe, M.J.1
  • 23
    • 33748683496 scopus 로고    scopus 로고
    • Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian procrustes problem
    • Theobald,D.L. and Wuttke,D.S. (2006a) Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian procrustes problem. Proc. Natl Acad. Sci. USA, 103, 18521-18527.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 18521-18527
    • Theobald, D.L.1    Wuttke, D.S.2
  • 24
    • 33748663254 scopus 로고    scopus 로고
    • THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures
    • Theobald,D.L. and Wuttke,D.S. (2006b) THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures. Bioinformatics, 22, 2171-2172.
    • (2006) Bioinformatics , vol.22 , pp. 2171-2172
    • Theobald, D.L.1    Wuttke, D.S.2
  • 26
    • 0029644728 scopus 로고
    • Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kmases
    • Vonrhein,C. et al. (1995) Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kmases. Structure, 3, 483-490.
    • (1995) Structure , vol.3 , pp. 483-490
    • Vonrhein, C.1
  • 27
    • 38349092279 scopus 로고    scopus 로고
    • Conformational transitions in adenylate kinase. Allosteric communication reduces misligation
    • Whitford,P.C. et al. (2008) Conformational transitions in adenylate kinase. Allosteric communication reduces misligation. J. Biol. Chem., 283, 2042-2048.
    • (2008) J. Biol. Chem , vol.283 , pp. 2042-2048
    • Whitford, P.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.