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Volumn 34, Issue WEB. SERV. ISS., 2006, Pages

Protein Block Expert (PBE): A web-based protein structure analysis server using a structural alphabet

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

EID: 33747831751     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl199     Document Type: Article
Times cited : (47)

References (28)
  • 2
    • 0030628304 scopus 로고    scopus 로고
    • Hierarchical protein structure superposition using both secondary structure and atomic representations
    • Singh,A.P. and Brutlag,D.L. (1997) Hierarchical protein structure superposition using both secondary structure and atomic representations. Proc. Int. Conf. Intell. Syst. Mol. Biol., 5, 284-293.
    • (1997) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.5 , pp. 284-293
    • Singh, A.P.1    Brutlag, D.L.2
  • 3
    • 0034479757 scopus 로고    scopus 로고
    • TOP: A new method for protein structure comparisons and similarity searches
    • Lu,G. (2000) TOP: a new method for protein structure comparisons and similarity searches. J. Appl. Crystallogr., 33, 176-183.
    • (2000) J. Appl. Crystallogr. , vol.33 , pp. 176-183
    • Lu, N.G.1
  • 4
    • 0033833116 scopus 로고    scopus 로고
    • Protein structure alignment using environmental profiles
    • Jung,J. and Lee,B. (2000) Protein structure alignment using environmental profiles. Protein Eng., 13, 535-543.
    • (2000) Protein Eng. , vol.13 , pp. 535-543
    • Jung, J.1    Lee, B.2
  • 5
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 6
    • 0022701772 scopus 로고
    • Using known substructures in protein model building and crystallography
    • Jones,T.A. and Thirup,S. (1986) Using known substructures in protein model building and crystallography. EMBO J., 5, 819-822.
    • (1986) EMBO J. , vol.5 , pp. 819-822
    • Jones, T.A.1    Thirup, S.2
  • 7
    • 0024395940 scopus 로고
    • A 3D building blocks approach to analyzing and predicting structure of proteins
    • Unger,R., Harel,D., Wherland,S. and Sussman,J.L. (1989) A 3D building blocks approach to analyzing and predicting structure of proteins. Proteins, 5, 355-373.
    • (1989) Proteins , vol.5 , pp. 355-373
    • Unger, R.1    Harel, D.2    Wherland, S.3    Sussman, J.L.4
  • 8
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • Levitt,M. (1992) Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol., 226, 507-533.
    • (1992) J. Mol. Biol. , vol.226 , pp. 507-533
    • Levitt, M.1
  • 9
    • 0027645984 scopus 로고
    • The importance of short structural motifs in protein structure analysis
    • Unger,R. and Sussman,J.L. (1993) The importance of short structural motifs in protein structure analysis. J. Comput. Aided Mol. Des., 7, 457-472.
    • (1993) J. Comput. Aided Mol. Des. , vol.7 , pp. 457-472
    • Unger, R.1    Sussman, J.L.2
  • 10
    • 0032555696 scopus 로고    scopus 로고
    • Prediction of local structure in proteins using a library of sequence-structure motifs
    • Bystroff,C. and Baker,D. (1998) Prediction of local structure in proteins using a library of sequence-structure motifs. J. Mol. Biol., 281, 565-577.
    • (1998) J. Mol. Biol. , vol.281 , pp. 565-577
    • Bystroff, C.1    Baker, D.2
  • 11
    • 0029063717 scopus 로고
    • The complexity and accuracy of discrete state models of protein structure
    • Park,B.H. and Levitt,M. (1995) The complexity and accuracy of discrete state models of protein structure. J. Mol. Biol., 249, 493-507.
    • (1995) J. Mol. Biol. , vol.249 , pp. 493-507
    • Park, B.H.1    Levitt, M.2
  • 12
    • 0036406112 scopus 로고    scopus 로고
    • Small libraries of protein fragments model native protein structures accurately
    • Kolodny,R., Koehl,P., Guibas,L. and Levitt,M. (2002) Small libraries of protein fragments model native protein structures accurately. J. Mol. Biol., 323, 297-307.
    • (2002) J. Mol. Biol. , vol.323 , pp. 297-307
    • Kolodny, R.1    Koehl, P.2    Guibas, L.3    Levitt, M.4
  • 13
    • 2942541294 scopus 로고    scopus 로고
    • Use of a structural alphabet for analysis of short loops connecting repetitive structures
    • Fourrier,L., Benros,C. and de Brevern,A.G. (2004) Use of a structural alphabet for analysis of short loops connecting repetitive structures. BMC Bioinformatics, 5, 58.
    • (2004) BMC Bioinformatics , vol.5 , pp. 58
    • Fourrier, L.1    Benros, C.2    de Brevern, A.G.3
  • 14
    • 0034669774 scopus 로고    scopus 로고
    • Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks
    • de Brevern,A.G., Etchebest,C. and Hazout,S. (2000) Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins, 41, 271-287.
    • (2000) Proteins , vol.41 , pp. 271-287
    • de Brevern, A.G.1    Etchebest, C.2    Hazout, S.3
  • 15
    • 23144437382 scopus 로고    scopus 로고
    • New assessment of a structural alphabet
    • de Brevern,A.G. (2005) New assessment of a structural alphabet. In Silico Biol., 5, 26.
    • (2005) Silico Biol. , vol.5 , pp. 26
    • de Brevern, A.G.1
  • 16
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 17
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 18
    • 3242891058 scopus 로고    scopus 로고
    • SA-Search: A web tool for protein structure mining based on a Structural Alphabet
    • Guyon,F., Camproux,A.C., Hochez,J. and Tuffery,P. (2004) SA-Search: a web tool for protein structure mining based on a Structural Alphabet. Nucleic Acids Res., 32, W545-W548.
    • (2004) Nucleic Acids Res. , vol.32
    • Guyon, F.1    Camproux, A.C.2    Hochez, J.3    Tuffery, P.4
  • 19
    • 0035175268 scopus 로고    scopus 로고
    • PALI - A database of Phylogeny and ALIgnment of homologous protein structures
    • Balaji,S., Sujatha,S., Kumar,S.S. and Srinivasan,N. (2001) PALI-a database of Phylogeny and ALIgnment of homologous protein structures. Nucleic Acids Res., 29, 61-65.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 61-65
    • Balaji, S.1    Sujatha, S.2    Kumar, S.S.3    Srinivasan, N.4
  • 20
    • 0037246028 scopus 로고    scopus 로고
    • Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database
    • Gowri,V.S., Pandit,S.B., Karthik,P.S., Srinivasan,N. and Balaji,S. (2003) Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database. Nucleic Acids Res., 31, 486-488.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 486-488
    • Gowri, V.S.1    Pandit, S.B.2    Karthik, P.S.3    Srinivasan, N.4    Balaji, S.5
  • 21
    • 0029860175 scopus 로고    scopus 로고
    • Local structural motifs of protein backbones are classified by self-organizing neural networks
    • Schuchhardt,J., Schneider,G., Reichelt,J., Schomburg,D. and Wrede,P. (1996) Local structural motifs of protein backbones are classified by self-organizing neural networks. Protein Eng., 9, 833-842.
    • (1996) Protein Eng. , vol.9 , pp. 833-842
    • Schuchhardt, J.1    Schneider, G.2    Reichelt, J.3    Schomburg, D.4    Wrede, P.5
  • 22
    • 0036893073 scopus 로고    scopus 로고
    • Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship
    • de Brevern,A.G., Valadie,H., Hazout,S. and Etchebest,C. (2002) Extension of a local backbone description using a structural alphabet: a new approach to the sequence-structure relationship. Protein Sci., 11, 2871-2886.
    • (2002) Protein Sci. , vol.11 , pp. 2871-2886
    • de Brevern, A.G.1    Valadie, H.2    Hazout, S.3    Etchebest, C.4
  • 23
    • 18844454820 scopus 로고    scopus 로고
    • A structural alphabet for local protein structures: Improved prediction methods
    • Etchebest,C., Benros,C., Hazout,S. and de Brevern,A.G. (2005) A structural alphabet for local protein structures: improved prediction methods. Proteins, 59, 810-827.
    • (2005) Proteins , vol.59 , pp. 810-827
    • Etchebest, C.1    Benros, C.2    Hazout, S.3    de Brevern, A.G.4
  • 24
    • 23144464778 scopus 로고    scopus 로고
    • A structural model of a seven-transmembrane helix receptor: The Duffy antigen/receptor for chemokine (DARC)
    • de Brevern,A.G., Wong,H., Tournamille,C., Colin,Y., Le Van Kim,C. and Etchebest,C. (2005) A structural model of a seven-transmembrane helix receptor: the Duffy antigen/receptor for chemokine (DARC). Biochim. Biophys. Acta, 1724, 288-306.
    • (2005) Biochim. Biophys. Acta , vol.1724 , pp. 288-306
    • de Brevern, A.G.1    Wong, H.2    Tournamille, C.3    Colin, Y.4    Le Van Kim, C.5    Etchebest, C.6
  • 25
    • 0028081403 scopus 로고
    • Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility
    • Russell,R.B. and Barton,G.J. (1994) Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility. J. Mol. Biol., 244, 332-350.
    • (1994) J. Mol. Biol. , vol.244 , pp. 332-350
    • Russell, R.B.1    Barton, G.J.2
  • 26
    • 0000009443 scopus 로고
    • Rapid Comparison of Protein Structres
    • McLachlan,A.D. (1982) Rapid Comparison of Protein Structres. Acta. Crystallogr., A38, 871-873.
    • (1982) Acta. Crystallogr. , vol.A38 , pp. 871-873
    • McLachlan, A.D.1
  • 28
    • 0033977581 scopus 로고    scopus 로고
    • The ASTRAL compendium for protein structure and sequence analysis
    • Brenner,S.E., Koehl,P. and Levitt,M. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 254-256
    • Brenner, S.E.1    Koehl, P.2    Levitt, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.