EpiDOCK: a molecular docking-based tool for MHC class II binding prediction

Mariyana Atanasova; Atanas Patronov; Ivan Dimitrov; Darren R. Flower; Irini Doytchinova

doi:10.1093/protein/gzt018

EpiDOCK: a molecular docking-based tool for MHC class II binding prediction

Mariyana Atanasova, Atanas Patronov, Ivan Dimitrov, Darren R. Flower, Irini Doytchinova^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

Abstract

Cellular peptide vaccines contain T-cell epitopes. The main prerequisite for a peptide to act as a T-cell epitope is that it binds to a major histocompatibility complex (MHC) protein. Peptide MHC binder identification is an extremely costly experimental challenge since human MHCs, named human leukocyte antigen, are highly polymorphic and polygenic. Here we present EpiDOCK, the first structure-based server for MHC class II binding prediction. EpiDOCK predicts binding to the 23 most frequent human, MHC class II proteins. It identifies 90% of true binders and 76% of true non-binders, with an overall accuracy of 83%. EpiDOCK is freely accessible at http://epidock.ddg-pharmfac. net.

Original language	English
Pages (from-to)	631-634
Number of pages	4
Journal	Protein Engineering, Design and Selection
Volume	26
Issue number	10
Early online date	9 May 2013
DOIs	https://doi.org/10.1093/protein/gzt018
Publication status	Published - Oct 2013

Keywords

docking
MHC class II binding prediction
peptide vaccines
quantitative matrices

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10.1093/protein/gzt018

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abstract = "Cellular peptide vaccines contain T-cell epitopes. The main prerequisite for a peptide to act as a T-cell epitope is that it binds to a major histocompatibility complex (MHC) protein. Peptide MHC binder identification is an extremely costly experimental challenge since human MHCs, named human leukocyte antigen, are highly polymorphic and polygenic. Here we present EpiDOCK, the first structure-based server for MHC class II binding prediction. EpiDOCK predicts binding to the 23 most frequent human, MHC class II proteins. It identifies 90% of true binders and 76% of true non-binders, with an overall accuracy of 83%. EpiDOCK is freely accessible at http://epidock.ddg-pharmfac. net.",

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T2 - a molecular docking-based tool for MHC class II binding prediction

AU - Atanasova, Mariyana

AU - Patronov, Atanas

AU - Dimitrov, Ivan

AU - Flower, Darren R.

AU - Doytchinova, Irini

PY - 2013/10

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AB - Cellular peptide vaccines contain T-cell epitopes. The main prerequisite for a peptide to act as a T-cell epitope is that it binds to a major histocompatibility complex (MHC) protein. Peptide MHC binder identification is an extremely costly experimental challenge since human MHCs, named human leukocyte antigen, are highly polymorphic and polygenic. Here we present EpiDOCK, the first structure-based server for MHC class II binding prediction. EpiDOCK predicts binding to the 23 most frequent human, MHC class II proteins. It identifies 90% of true binders and 76% of true non-binders, with an overall accuracy of 83%. EpiDOCK is freely accessible at http://epidock.ddg-pharmfac. net.

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KW - MHC class II binding prediction

KW - peptide vaccines

KW - quantitative matrices

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EpiDOCK: a molecular docking-based tool for MHC class II binding prediction

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