RPBS: A web resource for structural bioinformatics

Nucleic Acids Research

Volumn 33, Issue SUPPL. 2, 2005, Pages

  Alland, C ^d   Moreews, F ^d   Boens, D ^a   Carpentier, M ^b   Chiusa, S ^a   Lonquety, M ^a   Renault, N ^a   Wong, Y ^d   Cantalloube, H ^c   Chomilier, J ^a   Hochez, J ^d   Pothier, J ^b   Villoutreix, B O ^d   Zagury, J F ^c   Tuffery P ^d  

^a UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

^b SORBONNE UNIVERSITÉ   (France)

^c Bioinformatique et Chimie Moléculaire   (France)

^d INSERM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; INTERNET; PRIORITY JOURNAL; PROTEIN DATABASE; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; STRUCTURAL GENOMICS; FRANCE; INFORMATION PROCESSING; INFORMATION SERVICE; STRUCTURAL BIOINFORMATICS; WEB BROWSER; BIOLOGY; GENETIC DATABASE; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; STRUCTURAL HOMOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; INTERNET; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 23144443837     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki477     Document Type: Article

References (27)

1. Mucchielli-Giorgi,M.H., Hazout,S. and Tuffery,P. (2002) Predicting the disulfide bonding state of cysteines using protein descriptors. Proteins, 46, 243-249.
2. Fuchs,P.F.J. and Alix,A.J.P (2005) High accuracy prediction of beta-turns and their types using propensities and multiple alignments. Proteins, 59, 828-839.
3. Callebaut,I., Labesse,G., Durand,P., Poupon,A., Canard,L., ChomilierJ., Henrissat,B. and Mornon,J.P. (1997) Deciphering protein sequence information through hydrophobic cluster analysis (HCA): Current status and perspectives. Cell. Mol. Life Sci., 53, 621-645.
4. 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.
5. Mucchielli-Giorgi,M.H., Hazout,S. and Tuffery,P. (1999) PredAcc: prediction of solvent accessibility. Bioinformatics, 15, 176-177.
6. 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.
7. Gautier,R., Camproux,A.C. and Tuffery,P. (2004) SCit: Web tools for protein side chain conformation analysis. Nucleic Acid Res., 32, W508-W511.
8. Wojcik,J., Mornon,J.P. and Chomilier,J. (1999) New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. J. Mol. Biol., 289, 1469-1490.
9. Cantalloube,H., Nahum,C., Achour,A., Lehner,T., Callebaut,I., Burny,A., Bizzini,B., Mornon,J.P., Zagury,D. and Zagury,J.F. (1994) Automat: A novel software system for the systematic search for protein (or DNA) similarities with a notable application to autoimmune diseases and AIDS. Comput. Appl. Biosci., 10, 153-161.
10. Cantalloube,H., Labesse,G., Chomilier,J., Nahum,C., Cho,Y.Y., Chams,V., Achour,A., Lachgar,A., Mbika,J.P., Issing,W. and Zagury,J-F. (1995) Automat and BLAST: Comparison of two protein sequence similarity search programs. Comput. Appl. Biosci., 11, 261-272.
11. Cantalloube,H., Chomilier,J., Chiusa,S., Lonquety,M., Spadoni,J.L. and Zagury,J.F. (2005) Filtering redundancies for sequence similarity search programs. J. Biomol. Struct. Dyn., 22, 487-492.
12. Hubbard,T., Barker,D., Birney,E., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V., Down,T. et al. (2002) The Ensembl genome database project. Nucleic Acids Res., 30, 38-41.
13. Brenner,S.E., Koehl,P. and Levitt,M. (2000) The ASTRAL compendium for protein structure and sequence analysis. Nucleic Acids Res., 28, 254-256.
14. Wang,G. and Dunbrack,R.L.,Jr (2003) PISCES: A protein sequence culling server. Bioinformatics, 19, 1589-1591.
15. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
16. Levitt,M. (1976) A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol., 104, 59-107.
17. Aho,A.V. and Corasick,H.J. (1975) Efficient string matching: An aid to bibliographic search. Commun. ACM, 18, 333-340.
18. Raftery,A.E. (1985) A model for high-order markov chains. J. R. Stat. Soc. Ser B, 47, 528-539.
19. Novotny,M., Madsen,D. and Kleywegt,G.J. (2004) Evaluation of protein fold comparison servers. Proteins, 54, 260-270.
20. Carpentier,M., Brouillet,S. and Pothier,J. (2005) Yakusa: A fast structural database scanning method., Proteins, in press.
21. Fischer,D., Elofsson,A., Rice,D. and Eisenberg,D. (1996) Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pac. Symp. Biocomput., 300-318.
22. Deane,C.M. and Blundell,T.L. (2001) CODA: A combined algorithm for predicting the structurally variable regions of protein models. Protein Sci., 10, 599-612.
23. Fiser,A., Do,R.K. and Sali,A. (2003) Modeling of loops in protein structures. Protein Sci., 9, 1753-1773.
24. Kwasigroch,J.M., Chomilier,J. and Mornon,J.P. (1996) A global taxonomy of loops in globular proteins. J. Mol. Biol., 259, 855-872.
25. Brünger,A.T. (1988) Crystallographic refinement by simulated annealing: Application to a 2.8 Å resolution structure of aspartate aminotransferase. J. Mol. Biol., 203, 803-816.
26. Van Vlijmen,H.W. and Karplus,M. (1997) PDB-based protein loop prediction: Parameters for selection and methods for optimization. J. Mol. Biol., 267, 975-1001.
27. Rohl,C.A., Strauss,C.E., Chivian,D. and Baker,D. (2004) Modeling structurally variable regions in homologous proteins with rosetta. Proteins, 55, 656-677.