Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

Inferred Biomolecular Interaction Server--A Method and a Server to Analyze and Predict Protein Interacting Partners and Binding Sites

Recently we have developed a new database and method called "IBIS" (Inferred Biomolecular Interaction Server, http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi) which enables to conveniently study biomolecular interactions that have been observed in protein structures. Moreover, through inference by homology IBIS allows to formulate predictions/hypotheses for biomolecular interactions, even if the data for specific biomolecules is not available. Similar binding sites are clustered together based on their sequence and structure conservation. To emphasize biologically relevant binding sites, several algorithms are used for verification in terms of evolutionary conservation, biological importance of binding partners, size and stability of interfaces, as well as evidence from the published literature. IBIS organizes, analyzes and predicts interaction partners and locations of binding sites in proteins for five different types of binding partners (protein, chemical, nucleic acid, peptides and ions), and facilitates the mapping of a comprehensive biomolecular interaction network for a given protein query. The method was validated by comparison to other binding site prediction methods and to a collection of manually curated annotations. It has been shown that it achieves a sensitivity of about 72-75% at predicting biologically relevant sites for protein-small molecule and protein-protein interactions.

This research has been supported by the National Institutes of Health/DHHS (Intramural Research program of the National Library of Medicine).


  1. Shoemaker et al Nucleic Acids Res. Jan;38:D518-24 (2010).
  2. Thangudu et al BMC Bioinformatics Jul 1;11:365 (2010).

Benjamin A. Shoemaker
Dachuan Zhang
Ratna R. Thangudu
Manoj Tyagi
Jessica H. Fong
Aron Marchler-Bauer
Stephen H. Bryant
Thomas Madej
Anna R. Panchenko

National Center for Biotechnology Information
National Institutes of Health
Bethesda, MD 20894, USA

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