Novel developments with the PRINTS protein fingerprint database. (original) (raw)
- Journal List
- Nucleic Acids Res
- v.25(1); 1997 Jan 1
- PMC146411
Nucleic Acids Res. 1997 Jan 1; 25(1): 212–217.
Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WCIE 6BT, UK. attwood@bsm.bioc.ucl.ac.uk
Abstract
The PRINTS database of protein family 'fingerprints' is a diagnostic resource that complements the PROSITE dictionary of sites and patterns. Unlike regular expressions, fingerprints exploit groups of conserved motifs within sequence alignments to build characteristic signatures of family membership. Thus fingerprints inherently offer improved diagnostic reliability by virtue of the mutual context provided by motif neighbours. To date, 600 fingerprints have been constructed and stored in PRINTS, representing a 50% increase in the size of the database in the last year. The current version, 13.0, encodes approximately 3000 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is accessible via UCL's Bioinformatics World Wide Web (WWW) server at http://www.biochem.ucl.ac.uk/bsm/dbbrowser / . We describe here progress with the database, its Web interface, and a recent exciting development: the integration of a novel colour alignment editor (http://www.biochem.ucl.ac.uk/bsm/dbbrowser++ +/CINEMA ), which allows visualisation and interactive manipulation of PRINTS alignments over the Internet.
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Selected References
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- Bairoch A, Bucher P, Hofmann K. The PROSITE database, its status in 1995. Nucleic Acids Res. 1996 Jan 1;24(1):189–196. [PMC free article] [PubMed] [Google Scholar]
- Pietrokovski S, Henikoff JG, Henikoff S. The Blocks database--a system for protein classification. Nucleic Acids Res. 1996 Jan 1;24(1):197–200. [PMC free article] [PubMed] [Google Scholar]
- Parry-Smith DJ, Attwood TK. ADSP--a new package for computational sequence analysis. Comput Appl Biosci. 1992 Oct;8(5):451–459. [PubMed] [Google Scholar]
- Attwood TK, Findlay JB. Fingerprinting G-protein-coupled receptors. Protein Eng. 1994 Feb;7(2):195–203. [PubMed] [Google Scholar]
- Attwood TK, Beck ME, Bleasby AJ, Degtyarenko K, Parry Smith DJ. Progress with the PRINTS protein fingerprint database. Nucleic Acids Res. 1996 Jan 1;24(1):182–188. [PMC free article] [PubMed] [Google Scholar]
- Bleasby AJ, Akrigg D, Attwood TK. OWL--a non-redundant composite protein sequence database. Nucleic Acids Res. 1994 Sep;22(17):3574–3577. [PMC free article] [PubMed] [Google Scholar]
- Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res. 1996 Jan 1;24(1):21–25. [PMC free article] [PubMed] [Google Scholar]
- George DG, Barker WC, Mewes HW, Pfeiffer F, Tsugita A. The PIR-International Protein Sequence Database. Nucleic Acids Res. 1996 Jan 1;24(1):17–20. [PMC free article] [PubMed] [Google Scholar]
- Benson DA, Boguski M, Lipman DJ, Ostell J. GenBank. Nucleic Acids Res. 1996 Jan 1;24(1):1–5. [PMC free article] [PubMed] [Google Scholar]
- Pattabiraman N, Namboodiri K, Lowrey A, Gaber BP. NRL-3D: a sequence-structure database derived from the protein data bank (PDB) and searchable within the PIR environment. Protein Seq Data Anal. 1990 Oct;3(5):387–405. [PubMed] [Google Scholar]
- Parry-Smith DJ, Attwood TK. SOMAP: a novel interactive approach to multiple protein sequences alignment. Comput Appl Biosci. 1991 Apr;7(2):233–235. [PubMed] [Google Scholar]
- Sonnhammer EL, Kahn D. Modular arrangement of proteins as inferred from analysis of homology. Protein Sci. 1994 Mar;3(3):482–492. [PMC free article] [PubMed] [Google Scholar]
- Murvai J, Gabrielian A, Fábián P, Hátsagi Z, Degtyarenko K, Hegyi H, Pongor S. The SBASE protein domain library, Release 4.0: a collection of annotated protein sequence segments. Nucleic Acids Res. 1996 Jan 1;24(1):210–213. [PMC free article] [PubMed] [Google Scholar]
- Peitsch MC, Wells TN, Stampf DR, Sussman JL. The Swiss-3DImage collection and PDB-Browser on the World-Wide Web. Trends Biochem Sci. 1995 Feb;20(2):82–84. [PubMed] [Google Scholar]
- Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 1995 Apr 7;247(4):536–540. [PubMed] [Google Scholar]
- Kolakowski LF., Jr GCRDb: a G-protein-coupled receptor database. Receptors Channels. 1994;2(1):1–7. [PubMed] [Google Scholar]
- Attwood TK, Beck ME. PRINTS--a protein motif fingerprint database. Protein Eng. 1994 Jul;7(7):841–848. [PubMed] [Google Scholar]
- Attwood TK, Beck ME, Bleasby AJ, Parry-Smith DJ. PRINTS--a database of protein motif fingerprints. Nucleic Acids Res. 1994 Sep;22(17):3590–3596. [PMC free article] [PubMed] [Google Scholar]
- Michie AD, Jones ML, Attwood TK. DbBrowser: integrated access to databases worldwide. Trends Biochem Sci. 1996 May;21(5):191–191. [PubMed] [Google Scholar]
- Perkins DN, Attwood TK. XFINGER: a tool for searching and visualising protein fingerprints and patterns. Comput Appl Biosci. 1996 Apr;12(2):89–94. [PubMed] [Google Scholar]
- Flower DR, North AC, Attwood TK. Structure and sequence relationships in the lipocalins and related proteins. Protein Sci. 1993 May;2(5):753–761. [PMC free article] [PubMed] [Google Scholar]
- Flower DR, North AC, Attwood TK. Mouse oncogene protein 24p3 is a member of the lipocalin protein family. Biochem Biophys Res Commun. 1991 Oct 15;180(1):69–74. [PubMed] [Google Scholar]
- Boguski MS, Bairoch A, Attwood TK, Michaels GS. Proto-vav and gene expression. Nature. 1992 Jul 9;358(6382):113–113. [PubMed] [Google Scholar]
- Attwood TK, Findlay JB. Design of a discriminating fingerprint for G-protein-coupled receptors. Protein Eng. 1993 Feb;6(2):167–176. [PubMed] [Google Scholar]
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