SCOPEC: a database of protein catalytic domains

Motivation: Domains are the units of protein structure, function and evolution. It is therefore essential to utilize knowledge of domains when studying the evolution of function, or when assigning function to genome sequence data. For this purpose, we have developed a database of catalytic domains,...

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Vydáno v:	Bioinformatics Ročník 20; číslo suppl-1; s. i130 - i136
Hlavní autoři:	George, Richard A., Spriggs, Ruth V., Thornton, Janet M., Al-Lazikani, Bissan, Swindells, Mark B.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	England Oxford University Press 04.08.2004 Oxford Publishing Limited (England)
Témata:	Catalysis Computer Simulation Database Management Systems Databases, Protein Information Storage and Retrieval - methods Models, Chemical Protein Structure, Tertiary Proteins - chemistry Sequence Alignment - methods Sequence Analysis, Protein - methods
ISSN:	1367-4803, 1367-4811, 1460-2059, 1367-4811
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Shrnutí:	Motivation: Domains are the units of protein structure, function and evolution. It is therefore essential to utilize knowledge of domains when studying the evolution of function, or when assigning function to genome sequence data. For this purpose, we have developed a database of catalytic domains, SCOPEC, by combining structural domain information from SCOP, full-length sequence information from Swiss-Prot, and verified functional information from the Enzyme Classification (EC) database. Two major problems need to be overcome to create a database of domain–function relationships; (1) for sequences, EC numbers are typically assigned to whole sequences rather than the functional unit, and (2) The Protein Data Bank (PDB) structures elucidated from a larger multi-domain protein will often have EC annotation although the relevant catalytic domain may lie elsewhere. Results: SCOPEC entries have high quality enzyme assignments; having passed both computational and manual checks. SCOPEC currently contains entries for 75% of all EC annotations in the PDB. Overall, EC number is fairly well conserved within a superfamily, even when the proteins are distantly related. Initial analysis is encouraging; suggesting that there is a 50:50 chance of conserved function in distant homologues first detected by a third iteration PSI-BLAST search. Therefore, we envisage that a knowledge-based approach to function assignment using the domain–EC relationships in SCOPEC will gain a marked improvement over this base line. Availability: The SCOPEC database is a valuable resource in the analysis and prediction of protein structure and function. It can be obtained or queried at our website http://www.enzome.com
Bibliografie:	local:bth948 Contact: richardg@inpharmatica.co.uk ark:/67375/HXZ-P4P6N55L-T istex:08AD5D41261D5ACCC3CE5C1123CDBDC815B61F8D ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Article-2 ObjectType-Feature-1 content type line 23
ISSN:	1367-4803 1367-4811 1460-2059 1367-4811
DOI:	10.1093/bioinformatics/bth948