Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server.

Handle URI:
http://hdl.handle.net/10754/596812
Title:
Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server.
Authors:
Olimpieri, Pier Paolo; Chailyan, Anna; Tramontano, Anna; Marcatili, Paolo
Abstract:
MOTIVATION: Antibodies or immunoglobulins are proteins of paramount importance in the immune system. They are extremely relevant as diagnostic, biotechnological and therapeutic tools. Their modular structure makes it easy to re-engineer them for specific purposes. Short of undergoing a trial and error process, these experiments, as well as others, need to rely on an understanding of the specific determinants of the antibody binding mode. RESULTS: In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen. The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts. We believe that it can be of great help in re-design experiments as well as a guide for molecular docking experiments. The results that we obtained also allowed us to dissect which features of the antibody sequence contribute most to the involvement of specific residues in binding to the antigen. AVAILABILITY: http://www.biocomputing.it/proABC. CONTACT: anna.tramontano@uniroma1.it or paolo.marcatili@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Citation:
Olimpieri PP, Chailyan A, Tramontano A, Marcatili P (2013) Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server. Bioinformatics 29: 2285–2291. Available: http://dx.doi.org/10.1093/bioinformatics/btt369.
Publisher:
Oxford University Press (OUP)
Journal:
Bioinformatics
KAUST Grant Number:
KUK-I1-012-43
Issue Date:
26-Jun-2013
DOI:
10.1093/bioinformatics/btt369
PubMed ID:
23803466
PubMed Central ID:
PMC3753563
Type:
Article
ISSN:
1367-4803; 1460-2059
Sponsors:
KAUST Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST), FIRB RBIN06E9Z8_005, PRIN 20108XYHJS and the Epigenomics Flagship Project -EPIGEN.
Appears in Collections:
Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorOlimpieri, Pier Paoloen
dc.contributor.authorChailyan, Annaen
dc.contributor.authorTramontano, Annaen
dc.contributor.authorMarcatili, Paoloen
dc.date.accessioned2016-02-21T08:51:09Zen
dc.date.available2016-02-21T08:51:09Zen
dc.date.issued2013-06-26en
dc.identifier.citationOlimpieri PP, Chailyan A, Tramontano A, Marcatili P (2013) Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server. Bioinformatics 29: 2285–2291. Available: http://dx.doi.org/10.1093/bioinformatics/btt369.en
dc.identifier.issn1367-4803en
dc.identifier.issn1460-2059en
dc.identifier.pmid23803466en
dc.identifier.doi10.1093/bioinformatics/btt369en
dc.identifier.urihttp://hdl.handle.net/10754/596812en
dc.description.abstractMOTIVATION: Antibodies or immunoglobulins are proteins of paramount importance in the immune system. They are extremely relevant as diagnostic, biotechnological and therapeutic tools. Their modular structure makes it easy to re-engineer them for specific purposes. Short of undergoing a trial and error process, these experiments, as well as others, need to rely on an understanding of the specific determinants of the antibody binding mode. RESULTS: In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen. The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts. We believe that it can be of great help in re-design experiments as well as a guide for molecular docking experiments. The results that we obtained also allowed us to dissect which features of the antibody sequence contribute most to the involvement of specific residues in binding to the antigen. AVAILABILITY: http://www.biocomputing.it/proABC. CONTACT: anna.tramontano@uniroma1.it or paolo.marcatili@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.en
dc.description.sponsorshipKAUST Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST), FIRB RBIN06E9Z8_005, PRIN 20108XYHJS and the Epigenomics Flagship Project -EPIGEN.en
dc.publisherOxford University Press (OUP)en
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.comen
dc.rights.urihttp://creativecommons.org/licenses/by-nc/3.0en
dc.subject.meshSoftwareen
dc.titlePrediction of site-specific interactions in antibody-antigen complexes: the proABC method and server.en
dc.typeArticleen
dc.identifier.journalBioinformaticsen
dc.identifier.pmcidPMC3753563en
dc.contributor.institutionDepartment of Physics, Sapienza University and Istituto Pasteur - Fondazione Cenci Bolognetti, 00185 Rome, Italy.en
kaust.grant.numberKUK-I1-012-43en

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