IBIS (server) (Inferred Biomolecular Interaction Server) is a server developed at National Institutes of Health. It reports, predicts and integrates multiple types of conserved interactions for protein.

Philosophy

The knowledge of

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...

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
www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi
developed a
NCBI, National Institutes of Health
reports, predicts and integrates multiple types of conserved interactions for proteins. It provides tools to analyze

biomolecular A biomolecule or biological molecule is a loosely used term for molecules present in organisms that are essential to one or more typically biological processes, such as cell division, morphogenesis, or development. Biomolecules include large ...

interactions observed in a given protein structure together with the complex set of interactions inferred from its close

homologs A couple of homologous chromosomes, or homologs, are a set of one maternal and one paternal chromosome that pair up with each other inside a cell during fertilization. Homologs have the same genes in the same loci where they provide points alon ...

. 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 protein-protein, protein- small molecule, protein - nucleic acid, protein - peptide and protein - ion interactions. IBIS also allows the mapping of a biomolecular interaction network for any given organism, human interactome derived from structural complexes is available at ftp://ftp.ncbi.nih.gov/pub/mmdb/humanIntNw/. IBIS schema

To focus on biologically relevant

binding site In biochemistry and molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. The binding partner of the macromolecule is often referred to as a ligand. Ligands may inclu ...

s, 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. 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.

References

{{Reflist Servers (computing)