The PRINTS database: A fine-grained protein sequence annotation and analysis resource-its status in 2012

Database

Volumn 2012, Issue , 2012, Pages

  Attwood, Teresa K ^a   Coletta, Alain ^a   Muirhead, Gareth ^a   Pavlopoulou, Athanasia ^b   Philippou, Peter B ^a   Popov, Ivan ^c   Romá Mateo, Carlos ^d   Theodosiou, Athina ^b   Mitchell, Alex L ^a,e  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b BIOMEDICAL RESEARCH FOUNDATION   (Greece)

^c AGROBIOINSTITUTE   (Bulgaria)

^d CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE   (Spain)

^e WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; COMPUTER INTERFACE; GENETICS; HUMAN; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN DATABASE; PROTEIN MOTIF; SEQUENCE ALIGNMENT;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; CONSERVED SEQUENCE; DATABASES, PROTEIN; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PROTEINS; SEQUENCE ALIGNMENT; USER-COMPUTER INTERFACE;

EID: 84862252899     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bas019     Document Type: Article

References (39)

1. Akrigg, D. A., Attwood, T. K., Bleasby, A. J. et al. (1992) SERPENT - an information storage and analysis resource for protein sequences. CABIOS, 8, 295-296.
2. Bairoch, A. (1991) PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res., 19, 2241-2245.
3. Apweiler, R., Attwood, T. K., Bairoch, A. et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40. (Pubitemid 32054401)
4. Attwood, T. K., Beck, M. E., Bleasby, A. J. et al. (1994) PRINTS - A database of protein motif fingerprints. Nucleic Acids Res., 22, 3590-3596. (Pubitemid 24299831)
5. Sonnhammer, E. L., Eddy, S. R. and Durbin, R. (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins, 28, 405-420. (Pubitemid 27280344)
6. Attwood, T. K. (2001) A compendium of specific motifs for diagnosing GPCR subtypes. Trends Pharmacol. Sci., 22, 162-165. (Pubitemid 32244299)
7. Vaughan, S., Attwood, T. K., Navarro, M. et al. (2000) New tubulins in protozoal parasites. Curr. Biol., 10, R258-R259. (Pubitemid 30213372)
8. Moulton, G., Attwood, T. K., Parry-Smith, D. J. et al. (2003) Phylogenomic analysis and evolution of the potassium channel gene family. Recep. Chann., 9, 363-377. (Pubitemid 38008223)
9. Nordle, A. K., Rios, P., Gaulton, A. et al. (2007) Functional assignment of MAPK phosphatase domains. Proteins, 69, 19-31. (Pubitemid 47339136)
10. Roma-Mateo, C., Rios, P., Tabernero, L. et al. (2007) A novel phosphatase family, structurally related to dual-specificity phosphatases, that displays unique amino acid sequence and substrate specificity. J. Mol. Biol., 374, 899-909. (Pubitemid 350052102)
11. Attwood, T. K., Croning, M. D. R., Flower, D. R. et al. (2000) PRINTS-S: the database formerly known as PRINT S. Nucleic Acids Res., 28, 225-227. (Pubitemid 30047765)
12. Attwood, T. K., Bradley, P., Flower, D. R. et al. (2003) PRINTS and its automatic supplement, prePRINT S. Nucleic Acids Res., 31, 400-402. (Pubitemid 36150412)
13. Altschul, S. F., Gish, W., Miller, W. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
14. Wright, W., Scordis, P. and Attwood, T. K. (1999) BLAST PRINTS - an alternative perspective on sequence similarity. Bioinformatics, 15, 523-524. (Pubitemid 29361046)
15. Scordis, P., Flower, D. R. and Attwood, T. K. (1999) FingerPRINTScan: Intelligent searching of the PRINTS motif database. Bioinformatics, 15, 799-806. (Pubitemid 30055194)
16. Attwood, T. K., Blythe, M. J., Flower, D. R. et al. (2002) PRINTS and PRINTS-S shed light on protein ancestry. Nucleic Acids Res., 30, 239-241. (Pubitemid 34679553)
17. Henikoff, J., Greene, E. A., Pietrokovski, S. et al. (2000) Increased coverage of protein families with the Blocks Database servers. Nucleic Acids Res., 28, 228-230. (Pubitemid 30047766)
18. Huang, J. Y. and Brutlag, D. L. (2001) The EMOTIF database. Nucleic Acids Res., 29, 202-204. (Pubitemid 32054447)
19. Hunter, S., Jones, P., Mitchell, A. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res., 40, D306-D312.
20. UniProt Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71-D75.
21. Mi, H., Dong, Q., Muruganujan, A. et al. (2010) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res., 38, D204-D210.
22. Reich, J. R., Mitchell, A., Goble, C. A. et al. (2001) PRECIS: Protein Reports Engineered from Concise Information in SWISS-PRO T. IEEE Intell. Sys., 16, 42-51.
23. Divoli, A. and Attwood, T. K. (2005) BioIE: extracting informative sentences from the biomedical literature. Bioinformatics, 21, 2138-2139. (Pubitemid 40668070)
24. Mitchell, A. L., Divoli, A., Kim,J- H. et al. (2005) METIS: multiple extraction techniques for informative sentences. Bioinformatics, 21, 4196-4197. (Pubitemid 41672115)
25. Mitchell, A. L., Selimas, I. and Attwood, T. K. (2012) MINOTAUR: a web-based annotator-assistant tool. Int. J. Sys. Biol. Biomed. Technol., 1, 1-10.
26. Chen, J. G. and Ellis, B. E. (2008) GCR2 is a new member of the eukaryotic lanthionine synthetase component C-like protein family. Plant Signal Behav., 3, 307-310. (Pubitemid 351651937)
27. Wang, S. Z., Adler, R. and Nathans, J. (1992) A visual pigment from chicken that resembles rhodopsin: amino acid sequence, gene structure, and functional expression. Biochemistry, 31, 3309-3315.
28. Kawamura, S. and Yokoyama, S. (1995) Paralogous origin of the rhodopsin like opsin genes in lizards. J. Mol. Evol., 40, 594-600.
29. Shichida, Y., Imai, H., Imamoto, Y. et al. (1994) Is chicken greensensitive cone visual pigment a rhodopsin-like pigment? A comparative study of the molecular properties between chicken green and rhodopsin. Biochemistry, 33, 9040-9044. (Pubitemid 24272850)
30. Pettifer, S. R., Sinott, J. R. and Attwood, T. K. (2004) UTOPIA - userfriendly tools for operating informatics applications. Comp. Funct. Genomics, 5, CFG359.
31. Pettifer, S., Thorne, D., McDermott, P. et al. (2009) Visualising biological data: a semantic approach to tool and database integration. BMC Bioinformatics, 10, S18.
32. Pettifer, S., Thorne, D., McDermott, P. et al. (2009) An active registry for bioinformatics Web services. Bioinformatics, 25, 2090-2091.
33. Pettifer, S., Ison, J., Kalas, M. et al. (2010) The EMBRACE web service collection. Nucleic Acids Res., 38 (Web Server issue), W683-W688.
34. Bhagat, J., Tanoh, F., Nzuobontane, E. et al. (2010) BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Res., 38, W689-W694.
35. Sigrist, C. J., Cerutti, L., de Castro, E. et al. (2010) PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res., 38, D161-D166.
36. Wong, W. C., Maurer-Stroh, S. and Eisenhaber, F. (2010) More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PLoS Comput. Biol., 6, e1000867.
37. Schnoes, A. M., Brown, S. D., Dodevski, I. et al. (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput. Biol., 5, e1000605.
38. Gilks, W. R., Audit, B., de, A. D. et al. (2002) Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics, 18, 1641-1649. (Pubitemid 36097730)
39. Benson, D. A., Karsch-Mizrachi, I., Clark, K. et al. (2012) GenBank. Nucleic Acids Res., 40, D48-D53.