title: IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins.
abstract: We have recently developed the Inferred Biomolecular Interaction Server (IBIS) and database, which reports, predicts and integrates different types of interaction partners and locations of binding sites in proteins based on the analysis of homologous structural complexes. Here, we highlight several new IBIS features and options. The server's webpage is now redesigned to allow users easier access to data for different interaction types. An entry page is added to give a quick summary of available results and to now accept protein sequence accessions. To elucidate the formation of protein complexes, not just binary interactions, IBIS currently presents an expandable interaction network. Previously, IBIS provided annotations for four different types of binding partners: proteins, small molecules, nucleic acids and peptides; in the current version a new protein-ion interaction type has been added. Several options provide easy downloads of IBIS data for all Protein Data Bank (PDB) protein chains and the results for each query. In this study, we show that about one-third of all RefSeq sequences can be annotated with IBIS interaction partners and binding sites. The IBIS server is available at http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi and updated biweekly.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Building 38A, Bethesda, MD 20894, USA.
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Shoemaker
authors.forename: Dachuan
authors.initials: D
authors.lastname: Zhang
authors.forename: Manoj
authors.initials: M
authors.lastname: Tyagi
authors.forename: Ratna R
authors.initials: RR
authors.lastname: Thangudu
authors.forename: Jessica H
authors.initials: JH
authors.lastname: Fong
authors.forename: Aron
authors.initials: A
authors.lastname: Marchler-Bauer
authors.forename: Stephen H
authors.initials: SH
authors.lastname: Bryant
authors.forename: Thomas
authors.initials: T
authors.lastname: Madej
authors.forename: Anna R
authors.initials: AR
authors.lastname: Panchenko
mesh_terms: D001665:Binding Sites; D003196:Computer Graphics; D030562:Databases, Protein; D007477:Ions / Q000737:chemistry; D058977:Molecular Sequence Annotation; D046912:Multiprotein Complexes / Q000737:chemistry; D009696:Nucleic Acids / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D007477:Ions; D046912:Multiprotein Complexes; D009696:Nucleic Acids; D010455:Peptides; D011506:Proteins
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