SA-Search: A web tool for protien structure mining based on a Structural Alphabet

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Guyon, Frédéric ^a   Camproux, Anne Claude ^a   Hochez, Joëlle ^a   Tufféry, Pierre ^a  

^a INSERM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; INTERNET; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DATA BANK; PROTEIN STRUCTURE; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; INTERNET; MARKOV CHAINS; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 3242891058     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh467     Document Type: Article

References (15)

1. Gibrat,J.F., Madej,T. and Bryant,S.H. (1996) Surprising similarities in structure comparison. Curr. Opin. Struct. Biol., 6, 377-385.
2. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distances matrices. J. Mol. Biol., 233, 123-138.
3. Lapthrop,R.H. (1994) The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng., 7, 1059-1068.
4. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental Combinatorial Extension (CE) of the optimal path. Protein Eng., 11, 739-747.
5. Singh,A.P. and Brutlag,D.L. (1997) Hierarchical protein structure alignment using both secondary structure and atomic representations. The Sixth International Conference on Intelligent Systems for Molecular Biology (ISMB-97), 4, Halkidiki, Canada, 284-293.
6. Szustakowski,J.D. and Weng,Z. (2000) Protein structure alignment using a genetic algorithm. Proteins, 38, 428-440.
7. Zemla,A. (2003) LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.
8. Kawabata,T. (2003) MATRAS: a program for protein 3D structure comparison. Nucleic Acids Res., 31, 3367-3369.
9. Camproux,A.C., Tufféry,P., Chevrolat,J.P., Boisvieux,J.F. and Hazout,S. (1999) Hidden Markov model approach for identifying the modular framework of the protein backbone. Protein Eng., 12, 1063-1073.
10. Camproux,A.C., Gautier,R. and Tufféry,P. (2004) A hidden Markov model derived structural alphabet for proteins. J. Mol. Biol., doi: 10.1016/j.jmb.2004.04.005.
11. Baum,L.E., Petrie,T., Soules,G. and Weiss,N. (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann. Math. Stat., 41, 164-171.
12. Gusfield,D. (1997) Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge.
13. Smith,T.F. and Waterman,M. (1981) Identification of common molecular sequences. J. Mol. Biol., 147, 195-197.
14. Wang,G. and Dunbrack,R.L.Jr (2003) PISCES: a protein sequence culling server. Bioinformatics, 19, 1589-1591.
15. Andreeva,A., Howorth,D., Brenner,S.E., Hubbard,T.J.P., Chothia,C. and Murzin,A.G. (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acid Res., 32, D226-D229.