Recent improvements to the PROSITE database

Nucleic Acids Research

Volumn 32, Issue DATABASE ISS., 2004, Pages

  Hulo, Nicolas ^c   Sigrist, Christian J A ^c   Le Saux, Virginie ^c   Langendijk Genevaux, Petra S ^c   Bordoli, Lorenza ^a   Gattiker, Alexandre ^c   De Castro, Edouard ^c   Bucher, Philipp ^b   Bairoch, Amos ^c  

^a UNIVERSITY OF BASEL   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; DOCUMENTATION; HUMAN; INTERNET; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROSITE; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE;

AMINO ACID MOTIFS; ANIMALS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, PROTEIN; HUMANS; INTERNET; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEINS; QUALITY CONTROL; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0346869047     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (18)

1. Sigrist,C.J.A., Cerutti,L., Hulo,N., Gattiker,A., Falquet,L., Pagni,M., Bairoch,A. and Bucher,P. (2002) PROSITE: a documented database using patterns and profiles as motif descriptors. Brief. Bioinform., 3, 265-274.
2. Gribskov,M., Luthy,R. and Eisenberg,D. (1990) Profile analysis. Methods Enzymol., 183, 146-159.
3. Bucher,P., Karplus,K., Moeri,N. and Hofmann,K. (1996) A flexible motif search technique based on generalized profiles. Comput. Chem., 20, 3-23.
4. Hofmann,K. (2000) Sensitive protein comparisons with profiles and hidden Markov models. Brief. Bioinform, 1, 167-178.
5. Pagni,M. and Jongeneel,C.V. (2001) Making sense of score statistics for sequence alignments. Brief. Bioinform., 2, 51-67.
6. Gattiker,A., Gasteiger,E. and Bairoch,A. (2002) ScanProsite: a reference implementation of a PROSITE scanning tool. Appl. Bioinform, 1, 107-108.
7. Attwood,T.K., Bradley,P., Flower,D.R., Gaulton,A., Maudling,N., Mitchell,A.L., Moulton,G., Nordle,A., Paine,K., Taylor,P. et al. (2003) PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res., 31, 400-402.
8. Mulder,N.J., Apweiler,R., Attwood,T.K., Bairoch,A., Barrell,D., Bateman,A., Binns,D., Biswas,M., Bradley,P., Bork,P. et al. (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res., 31, 315-318.
9. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
10. Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
11. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
12. Sjolander,K., Karplus,K, Brown,M., Hughey,R., Krogh,A., Mian,I.S. and Haussler,D. (1996) Dirichlet mixtures: a method for improved detection of weak but significant protein sequence homology. Comput. Appl. Biosci., 12, 327-345.
13. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
14. Jonassen,I. (1997) Efficient discovery of conserved patterns using a pattern graph. Comput. Appl. Biosci., 13, 509-522.
15. Apweiler,R. Bairoch,A., Wu,C.H. Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H., Lopez, R., Magrane,M. et al. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res., 32, D115-D119.
16. Sayle,R.A. and Milner-White,E.J. (1995) RASMOL: biomolecular graphics for all. Trends Biochem. Sci., 20, 374.
17. Pagni,M., Iseli,C., Junier,T., Falquet,L., Jongeneel,V. and Bucher,P. (2001) trEST, trGEN and Hits: access to databases of predicted protein sequences. Nucleic Acids Res., 29, 148-151.
18. Falquet,L., Pagni,M., Bucher,P., Hulo,N., Sigrist,C.J.A., Hofmann,K. and Bairoch,A. (2002) The PROSITE database, its status in 2002. Nucleic Acids Res., 30, 235-238.