EyeSite: A semi-automated database of protein families in the eye

Nucleic Acids Research

Volumn 32, Issue DATABASE ISS., 2004, Pages

  Lee, David A ^a,b   Fefeu, Sandrine ^a   Edo Ukeh, Adrian A ^a,b   Orengo, Christine A ^b   Slingsby, Christine ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EYE PROTEIN;

ALGORITHM; ALLELE; ARTICLE; AUTOMATION; BIOINFORMATICS; CATH; DATA BASE; EYESITE; GENE CLUSTER; GENETIC VARIABILITY; HUMAN; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERNET; MOLECULAR MODEL; ONLINE SYSTEM; PFAM; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; TISSUE TYPES;

AMINO ACID SEQUENCE; ANIMALS; AUTOMATION; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EYE; EYE PROTEINS; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; ORGAN SPECIFICITY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 0345864016     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (18)

1. Wistow,G. (2002) A project for ocular bioinformatics: NEIBank. Mol. Vis., 8, 161-163.
2. Minoshima,S., Mitsuyama,S., Ohno,S., Kawamura,T. and Shimizu,N. (2000) Eye Disorder Database 'KmeyeDB'. Hum. Mutat., 15, 95-98.
3. Pearl,F.M., Bennett,C.F., Bray,J.E., Harrison,A.P., Martin,N., Shepherd,A., Sillitoe,I., Thornton,J. and Orengo,C.A. (2003) The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res., 31, 452-455.
4. LoConte,L., Brenner,S.E., Hubbard,T.J., Chothia,C. and Murzin,A.G. (2002) SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res., 30, 264-267.
5. Buchan,D.W., Shepherd,A.J., Lee,D., Pearl,F.M., Rison,S.C., Thornton,J.M. and Orengo,C.A. (2002) Gene3D: structural assignments for whole genes and genomes using the CATH domain structure database. Genome Res., 12, 503-14.
6. Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L. L. (2002) The Pfam Protein Families Database. Nucleic Acids Res., 30, 276-280.
7. Vitkup,D., Melamud,E., Moult,J. and Sander,C. (2001) Completeness in structural genomics. Nature Struct. Biol., 8, 559-566.
8. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J., Rapp,B.A. and Wheeler,L. (2000) GenBank. Nucleic Acids Res., 28, 15-18.
9. Enright,A.J., Van Dongen,S. and Ouzounis,C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
10. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.-C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan, I., Pilbout,S. and Schneider,M. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
11. Pruitt,K.D. and Maglott,D.R. (2001) RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res., 29, 137-140.
12. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
13. Higgins,D. Thompson,J., Gibson,T., Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTALW: improving the sensitivity of progressive multiple alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
14. Karplus,K., Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
15. Pearl,F.M.G., Lee,D., Bray,J.E., Sillitoe,I., Todd,A.E., Harrison,A.P., Thornton,J.M. and Orengo,C.A. (2000) Assigning genomic sequences to CATH. Nucleic Acids Res., 28, 277-282.
16. 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.
17. Marti-Renom,M.A., Stuart,A., Fiser,A., Sánchez,R., Melo,F. and Šali,A. (2000) Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct., 29, 291-325.
18. Shepherd,A.J., Martin,N.J., Johnson,R.G., Kellam,P. and Orengo,C.A. (2002) PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources. Bioinformatics, 18, 1666-1672.