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SDDB uses previously calculated and stored HMM descriptors for predicting active sites, binding residues, and protein function. The database integrates biologically relevant data filtered from several databases such as PDB, PDBSUM, CSA and SCOP. It accepts queries in fasta format and predicts functional residue positions, protein-ligand interactions, and protein function, based on the SCOP database.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>To assess the SDDB performance, we used different data sets. The Trypsion-like Serine protease data set assessed how well SDDB predicts functional sites when curated data is available. The SCOP family data set was used to analyze SDDB performance by using training data extracted from PDBSUM (binding sites) and from CSA (active sites). The ATP-binding experiment was used to compare our approach with the most current method. For all evaluations, significant improvements were obtained with SDDB.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>SDDB performed better when trusty training data was available. SDDB worked better in predicting active sites rather than binding sites because the former are more conserved than the latter. Nevertheless, by using our prediction method we obtained results with precision above 70%.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-492","type":"journal-article","created":{"date-parts":[[2008,11,25]],"date-time":"2008-11-25T19:14:00Z","timestamp":1227640440000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Structural descriptor database: a new tool for sequence-based functional site prediction"],"prefix":"10.1186","volume":"9","author":[{"given":"Juliana S","family":"Bernardes","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jorge H","family":"Fernandez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ana Tereza R","family":"Vasconcelos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,11,25]]},"reference":[{"key":"2477_CR1","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1126\/science.1121018","volume":"311","author":"J Chandonia","year":"2006","unstructured":"Chandonia J, Brenner S: The impact of structural genomics: expectations and outcomes. 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