User:Kalapat/sandbox

The knowledge of protein structures may facilitate and improve the annotation of protein function and the characterization of protein binding partners and binding sites. A database and server IBIS (Inferred Biomolecular Interaction Server), http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.html, provides tools to analyze biomolecular interactions observed in a given protein structure together with the complex set of interactions inferred from its close homologs. IBIS identifies and predicts proteins' interaction partners together with the locations of the corresponding binding sites on the protein query. It provides annotations of binding sites for proteins, small chemicals, nucleic acids, peptides and ions. This may allow the mapping of a biomolecular interaction network for a given organism ftp://ftp.ncbi.nih.gov/pub/mmdb/humanIntNw/.

To focus on biologically relevant binding sites, IBIS clusters similar binding sites found in homologous proteins based on the sites’ conservation of sequence and structure. Binding sites which appear evolutionarily conserved among non-redundant sets of homologous proteins are given higher priority in the displays. Additionally, binding site clusters are validated by comparing them with binding site annotations from a manually curated subset of the Conserved Domain Database (CDD), if available. In the case of protein–protein binding sites, IBIS compares its findings to binding interfaces confirmed by the PISA algorithm, which estimates the stability of protein-protein interfaces observed in crystal structures. After binding sites are clustered, position specific score matrices (PSSMs) are constructed from the corresponding binding site alignments. Together with other measures, the PSSMs are subsequently used to rank binding sites to assess how well they match the query, and to gauge the biological relevance of binding sites with respect to the query.