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2008

Structural descriptor database: a new tool for sequence-based functional site prediction

8 years 9 months ago
Structural descriptor database: a new tool for sequence-based functional site prediction
Background: The Structural Descriptor Database (SDDB) is a web-based tool that predicts the function of proteins and functional site positions based on the structural properties of related protein families. Structural alignments and functional residues of a known protein set (defined as the training set) are used to build special Hidden Markov Models (HMM) called HMM descriptors. 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. Results: 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 dat...
Juliana S. Bernardes, Jorge H. Fernandez, Ana Tere
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Juliana S. Bernardes, Jorge H. Fernandez, Ana Tereza R. Vasconcelos
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