| PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. | |
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MedLine Citation:
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PMID: 18443018 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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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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Authors:
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Michael J Sweredoski; Pierre Baldi |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. Date: 2008-04-28 |
Journal Detail:
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Title: Bioinformatics (Oxford, England) Volume: 24 ISSN: 1367-4811 ISO Abbreviation: Bioinformatics Publication Date: 2008 Jun |
Date Detail:
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Created Date: 2008-06-16 Completed Date: 2008-07-10 Revised Date: 2009-11-04 |
Medline Journal Info:
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Nlm Unique ID: 9808944 Medline TA: Bioinformatics Country: England |
Other Details:
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Languages: eng Pagination: 1459-60 Citation Subset: IM |
Affiliation:
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Department of Computer Science and Institute for Genomics and Bioinformatics, University of California, Irvine, California 92697-3435, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms* Amino Acid Sequence Epitope Mapping / methods* Epitopes, B-Lymphocyte / chemistry*, immunology* Molecular Sequence Data Sequence Analysis, Protein / methods* Software* |
| Grant Support | |
ID/Acronym/Agency:
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LM-07443-01/LM/NLM NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/Epitopes, B-Lymphocyte |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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