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Improving B-cell epitope prediction and its application to global antibody-antigen docking.
- Source :
-
Bioinformatics (Oxford, England) [Bioinformatics] 2014 Aug 15; Vol. 30 (16), pp. 2288-94. Date of Electronic Publication: 2014 Apr 21. - Publication Year :
- 2014
-
Abstract
- Motivation: Antibodies are currently the most important class of biopharmaceuticals. Development of such antibody-based drugs depends on costly and time-consuming screening campaigns. Computational techniques such as antibody-antigen docking hold the potential to facilitate the screening process by rapidly providing a list of initial poses that approximate the native complex.<br />Results: We have developed a new method to identify the epitope region on the antigen, given the structures of the antibody and the antigen-EpiPred. The method combines conformational matching of the antibody-antigen structures and a specific antibody-antigen score. We have tested the method on both a large non-redundant set of antibody-antigen complexes and on homology models of the antibodies and/or the unbound antigen structure. On a non-redundant test set, our epitope prediction method achieves 44% recall at 14% precision against 23% recall at 14% precision for a background random distribution. We use our epitope predictions to rescore the global docking results of two rigid-body docking algorithms: ZDOCK and ClusPro. In both cases including our epitope, prediction increases the number of near-native poses found among the top decoys.<br />Availability and Implementation: Our software is available from http://www.stats.ox.ac.uk/research/proteins/resources.<br /> (© The Author 2014. Published by Oxford University Press.)
Details
- Language :
- English
- ISSN :
- 1367-4811
- Volume :
- 30
- Issue :
- 16
- Database :
- MEDLINE
- Journal :
- Bioinformatics (Oxford, England)
- Publication Type :
- Academic Journal
- Accession number :
- 24753488
- Full Text :
- https://doi.org/10.1093/bioinformatics/btu190