SCOPEC: a database of protein catalytic domains Export

@article{citeulike:388250, abstract = {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 10.1093/bioinformatics/bth948}, address = {Inpharmatica Ltd, 60 Charlotte street, London W1T 2NU, UK.}, author = {George, Richard A. and Spriggs, Ruth V. and Thornton, Janet M. and Al-Lazikani, Bissan and Swindells, Mark B.}, citeulike-article-id = {388250}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/bth948}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/20/suppl_1/i130.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/20/suppl_1/i130.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/suppl_1/i130}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/15262791}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=15262791}, day = {4}, doi = {10.1093/bioinformatics/bth948}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {cat\_res, database, domains, inpharmatica}, month = {August}, number = {suppl\_1}, pages = {i130--136}, posted-at = {2005-11-11 15:32:40}, priority = {2}, title = {SCOPEC: a database of protein catalytic domains}, url = {http://dx.doi.org/10.1093/bioinformatics/bth948}, volume = {20}, year = {2004} }

TY - JOUR ID - citeulike:388250 L3 - citeulike-article-id:388250 N2 - 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 10.1093/bioinformatics/bth948 IS - suppl_1 JF - Bioinformatics SN - 1367-4803 AD - Inpharmatica Ltd, 60 Charlotte street, London W1T 2NU, UK. EP - 136 TI - SCOPEC: a database of protein catalytic domains VL - 20 SP - i130 KW - cat_res KW - database KW - domains KW - inpharmatica AU - George, Richard AU - Spriggs, Ruth AU - Thornton, Janet AU - Al-Lazikani, Bissan AU - Swindells, Mark PY - 2004/08/04/ UR - http://dx.doi.org/10.1093/bioinformatics/bth948 ER -