Michael J Sweredoski1, Pierre Baldi. 1. Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697-3435, USA.
Abstract
MOTIVATION: Accurate prediction of B-cell epitopes is an important goal of computational immunology. Up to 90% of B-cell epitopes are discontinuous in nature, yet most predictors focus on linear epitopes. Even when the tertiary structure of the antigen is available, the accurate prediction of B-cell epitopes remains challenging. RESULTS: Our predictor, PEPITO, uses a combination of amino-acid propensity scores and half sphere exposure values at multiple distances to achieve state-of-the-art performance. PEPITO achieves an area under the curve (AUC) of 75.4 on the Discotope dataset. Additionally, we benchmark PEPITO as well as the Discotope predictor on the more recent Epitome dataset, achieving AUCs of 68.3 and 66.0, respectively. AVAILABILITY: PEPITO is available as part of the SCRATCH suite of protein structure predictors via www.igb.uci.edu. CONTACT: pfbaldi@ics.uci.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Accurate prediction of B-cell epitopes is an important goal of computational immunology. Up to 90% of B-cell epitopes are discontinuous in nature, yet most predictors focus on linear epitopes. Even when the tertiary structure of the antigen is available, the accurate prediction of B-cell epitopes remains challenging. RESULTS: Our predictor, PEPITO, uses a combination of amino-acid propensity scores and half sphere exposure values at multiple distances to achieve state-of-the-art performance. PEPITO achieves an area under the curve (AUC) of 75.4 on the Discotope dataset. Additionally, we benchmark PEPITO as well as the Discotope predictor on the more recent Epitome dataset, achieving AUCs of 68.3 and 66.0, respectively. AVAILABILITY: PEPITO is available as part of the SCRATCH suite of protein structure predictors via www.igb.uci.edu. CONTACT: pfbaldi@ics.uci.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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