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Nucleic Acids Research Advance Access published online on October 20, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp842
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Published by Oxford University Press 2009.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites

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

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

*To whom correspondence should be addressed. Tel: +1 301 435 5891; Fax: +1 301 480 4637; Email: panch{at}ncbi.nlm.nih.gov Correspondence may also be addressed to Thomas Madej. Tel: +1 301 435 5998; Fax: +1 301 480 4637; Email: madej{at}ncbi.nlm.nih.gov

Received August 15, 2009. Revised September 16, 2009. Accepted September 21, 2009.

IBIS is the NCBI Inferred Biomolecular Interaction Server. This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins. IBIS provides annotations for different types of binding partners (protein, chemical, nucleic acid and peptides), and facilitates the mapping of a comprehensive biomolecular interaction network for a given protein query. IBIS reports interactions observed in experimentally determined structural complexes of a given protein, and at the same time IBIS infers binding sites/interacting partners by inspecting protein complexes formed by homologous proteins. 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 is updated regularly and is freely accessible via http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.html.


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