Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server.
Bioinformatics
; 29(18): 2285-91, 2013 Sep 15.
Article
in En
| MEDLINE
| ID: mdl-23803466
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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Software
/
Antigen-Antibody Complex
Type of study:
Evaluation_studies
/
Prognostic_studies
/
Risk_factors_studies
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2013
Type:
Article
Affiliation country:
Italy