Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure

Kunik, V., Ashkenazi, S. and Ofran, Y. (2012) Paratome: an online tool for systematic identification of antigen-binding regions in antibodies based on sequence or structure. Nucleic Acids Research, 40(W1), W521-W524. (doi: 10.1093/nar/gks480) (PMID:22675071) (PMCID:PMC3394289)

Abstract

Antibodies are capable of specifically recognizing and binding antigens. Identification of the antigen-binding site, commonly dubbed paratope, is of high importance both for medical and biological applications. To date, the identification of antigen-binding regions (ABRs) relies on tools for the identification of complementarity-determining regions (CDRs). However, we have shown that up to 22% of the residues that actually bind the antigen fall outside the traditionally defined CDRs. The Paratome web server predicts the ABRs of an antibody, given its amino acid sequence or 3D structure. It is based on a set of consensus regions derived from a structural alignment of a non-redundant set of all known antibody–antigen complexes. Given a query sequence or structure, the server identifies the regions in the query antibody that correspond to the consensus ABRs. An independent set of antibody–antigen complexes was used to test the server and it was shown to correctly identify at least 94% of the antigen-binding residues. The Paratome web server is freely available at http://www.ofranlab.org/paratome/.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Ashkenazi, Shaul
• Authors: Kunik, V., Ashkenazi, S., and Ofran, Y.
• College/School: College of Science and Engineering > School of Computing Science
• Journal Name: Nucleic Acids Research
• Publisher: Oxford University Press
• ISSN: 0305-1048
• ISSN (Online): 1362-4962
• Published Online: 06 June 2012
• Copyright Holders: Copyright © 2012 The Authors
• First Published: First published in Nucleic Acids Research 40(W1): W521-W524
• Publisher Policy: Reproduced under a Creative Commons License