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Volumn 39, Issue SUPPL. 1, 2011, Pages

PCDB: A database of protein conformational diversity

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLASSIFICATION ALGORITHM; CRYSTAL STRUCTURE; INFORMATION PROCESSING; MUTATION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN CONFORMATIONAL DIVERSITY DATABASE; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FUNCTION; TAXONOMY;

EID: 78651327630     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1181     Document Type: Article
Times cited : (25)

References (43)
  • 1
  • 2
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • Henzler-Wildman,K.A.,Lei,M.,Thai,V.,Kerns,S.J.,Karplus,M. and Kern,D. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature,450,913-916.
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.A.1    Lei, M.2    Thai, V.3    Kerns, S.J.4    Karplus, M.5    Kern, D.6
  • 5
    • 43649093747 scopus 로고    scopus 로고
    • Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations
    • Yogurtcu,O.N.,Erdemli,S.B.,Nussinov,R.,Turkay,M. and Keskin,O. (2008) Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations. Biophys. J.,94,3475-3485.
    • (2008) Biophys. J. , vol.94 , pp. 3475-3485
    • Yogurtcu, O.N.1    Erdemli, S.B.2    Nussinov, R.3    Turkay, M.4    Keskin, O.5
  • 7
    • 0347753736 scopus 로고    scopus 로고
    • Ligand-dependent dynamics and intramolecular signaling in a PDZ domain
    • Fuentes,E.J.,Der,C.J. and Lee,A.L. (2004) Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. J. Mol. Biol.,335,1105-1115.
    • (2004) J. Mol. Biol. , vol.335 , pp. 1105-1115
    • Fuentes, E.J.1    Der, C.J.2    Lee, A.L.3
  • 11
    • 64849111005 scopus 로고    scopus 로고
    • Sending signals dynamically
    • Smock,R.G. and Gierasch,L.M. (2009) Sending signals dynamically. Science,324,198-203.
    • (2009) Science , vol.324 , pp. 198-203
    • Smock, R.G.1    Gierasch, L.M.2
  • 12
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • Tokuriki,N. and Tawfik,D.S. (2009) Protein dynamism and evolvability. Science,324,203-207.
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 15
    • 73949129925 scopus 로고    scopus 로고
    • Coarse-grained models reveal functional dynamics-II. Molecular dynamics simulation at the coarse-grained level: Theories and biological applications
    • Chng,C.P. and Yang,L.W. (2008) Coarse-grained models reveal functional dynamics-II. Molecular dynamics simulation at the coarse-grained level: theories and biological applications. Bioinform. Biol. Insights,2,171-185.
    • (2008) Bioinform. Biol. Insights , vol.2 , pp. 171-185
    • Chng, C.P.1    Yang, L.W.2
  • 16
    • 18744371588 scopus 로고    scopus 로고
    • Molecular dynamics and protein function
    • Karplus,M. and Kuriyan,J. (2005) Molecular dynamics and protein function. Proc. Natl Acad. Sci. USA,102,6679-6685.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 6679-6685
    • Karplus, M.1    Kuriyan, J.2
  • 17
    • 17044393884 scopus 로고    scopus 로고
    • Coarse-grained models for proteins
    • Tozzini,V. (2005) Coarse-grained models for proteins. Curr. Opin. Struct. Biol.,15,144-150.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 144-150
    • Tozzini, V.1
  • 18
    • 25844431698 scopus 로고    scopus 로고
    • Coarse-grained normal mode analysis in structural biology
    • Bahar,I. and Rader,A.J. (2005) Coarse-grained normal mode analysis in structural biology. Curr. Opin. Struct. Biol.,15,586-592.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 586-592
    • Bahar, I.1    Rader, A.J.2
  • 19
    • 14844286108 scopus 로고    scopus 로고
    • Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
    • Ma,J. (2005) Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure,13,373-380.
    • (2005) Structure , vol.13 , pp. 373-380
    • Ma, J.1
  • 20
    • 0036298514 scopus 로고    scopus 로고
    • Relation between sequence and structure of HIV-1 protease inhibitor complexes: A model system for the analysis of protein flexibility
    • Zoete,V.,Michielin,O. and Karplus,M. (2002) Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J. Mol. Biol.,315,21-52.
    • (2002) J. Mol. Biol. , vol.315 , pp. 21-52
    • Zoete, V.1    Michielin, O.2    Karplus, M.3
  • 22
    • 37849031192 scopus 로고    scopus 로고
    • Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments
    • Kondrashov,D.A.,Zhang,W.,Roman Aranda IV,Stec,B. and Phillips,G.N. Jr (2008) Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Proteins,70,353-362.
    • (2008) Proteins , vol.70 , pp. 353-362
    • Kondrashov, D.A.1    Zhang, W.2    Roman Aranda, I.V.3    Stec, B.4    Phillips Jr., G.N.5
  • 23
    • 67049155677 scopus 로고    scopus 로고
    • A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family
    • Friedland,G.D.,Lakomek,N.A.,Griesinger,C.,Meiler,J. and Kortemme,T. (2009) A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput. Biol.,5,e1000393.
    • (2009) PLoS Comput. Biol. , vol.5
    • Friedland, G.D.1    Lakomek, N.A.2    Griesinger, C.3    Meiler, J.4    Kortemme, T.5
  • 24
    • 65349101761 scopus 로고    scopus 로고
    • Heterogeneity and dynamics in villin headpiece crystal structures
    • Meng,J. and McKnight,C.J. (2009) Heterogeneity and dynamics in villin headpiece crystal structures. Acta Crystallogr. D Biol. Crystallogr.,65,470-476.
    • (2009) Acta Crystallogr. D Biol. Crystallogr. , vol.65 , pp. 470-476
    • Meng, J.1    McKnight, C.J.2
  • 25
    • 70449923870 scopus 로고    scopus 로고
    • A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR,X-ray,and computations
    • Liu,L.,Koharudin,L.M.,Gronenborn,A.M. and Bahar,I. (2009) A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR,X-ray,and computations. Proteins,77,927-939.
    • (2009) Proteins , vol.77 , pp. 927-939
    • Liu, L.1    Koharudin, L.M.2    Gronenborn, A.M.3    Bahar, I.4
  • 26
    • 0037457815 scopus 로고    scopus 로고
    • Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics
    • Prabhu,N.V.,Lee,A.L.,Wand,A.J. and Sharp,K.A. (2003) Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics. Biochemistry,42,562-570.
    • (2003) Biochemistry , vol.42 , pp. 562-570
    • Prabhu, N.V.1    Lee, A.L.2    Wand, A.J.3    Sharp, K.A.4
  • 27
    • 18144378006 scopus 로고    scopus 로고
    • What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis
    • Best,R.B.,Clarke,J. and Karplus,M. (2005) What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis. J. Mol. Biol.,349,185-203.
    • (2005) J. Mol. Biol. , vol.349 , pp. 185-203
    • Best, R.B.1    Clarke, J.2    Karplus, M.3
  • 28
    • 67649795139 scopus 로고    scopus 로고
    • Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure
    • Burra,P.V.,Zhang,Y.,Godzik,A. and Stec,B. (2009) Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure. Proc. Natl Acad. Sci. USA,106,10505-10510.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 10505-10510
    • Burra, P.V.1    Zhang, Y.2    Godzik, A.3    Stec, B.4
  • 31
    • 12344307441 scopus 로고    scopus 로고
    • Conformational changes observed in enzyme crystal structures upon substrate binding
    • Gutteridge,A. and Thornton,J. (2005) Conformational changes observed in enzyme crystal structures upon substrate binding. J. Mol. Biol.,346,21-28.
    • (2005) J. Mol. Biol. , vol.346 , pp. 21-28
    • Gutteridge, A.1    Thornton, J.2
  • 32
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • Kumar,S.,Ma,B.,Tsai,C.J.,Sinha,N. and Nussinov,R. (2000) Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci.,9,10-19.
    • (2000) Protein Sci. , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 33
    • 1342302339 scopus 로고    scopus 로고
    • Conformational changes associated with protein-protein interactions
    • Goh,C.S.,Milburn,D. and Gerstein,M. (2004) Conformational changes associated with protein-protein interactions. Curr. Opin. Struct. Biol.,14,104-109.
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 104-109
    • Goh, C.S.1    Milburn, D.2    Gerstein, M.3
  • 34
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia,C. and Lesk,A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J.,5,823-826.
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 36
    • 0033963089 scopus 로고    scopus 로고
    • The ENZYME database in 2000
    • Bairoch,A. (2000) The ENZYME database in 2000. Nucleic Acids Res.,28,304-305.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 304-305
    • Bairoch, A.1
  • 37
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data
    • Porter,C.T.,Bartlett,G.J. and Thornton,J.M. (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res.,32,D129-133.
    • (2004) Nucleic Acids Res. , vol.32
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 40
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (matching molecular models obtained from theory): An automated method for model comparison
    • Ortiz,A.R.,Strauss,C.E. and Olmea,O. (2002) MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci.,11,2606-2621.
    • (2002) Protein Sci. , vol.11 , pp. 2606-2621
    • Ortiz, A.R.1    Strauss, C.E.2    Olmea, O.3
  • 41
    • 75849153303 scopus 로고    scopus 로고
    • The universal protein resource (uniprot) in 2010
    • The UniProt Consortium.
    • The UniProt Consortium. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res.,38,D142-148.
    • (2010) Nucleic Acids Res. , vol.38
  • 42
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular motions
    • Gerstein,M. and Krebs,W. (1998) A database of macromolecular motions. Nucleic Acids Res.,26,4280-4290.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.2


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