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 journalArticlepeer-review


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 languageEnglish
Pages (from-to)631-634
Number of pages4
JournalProtein Engineering, Design and Selection
Issue number10
Early online date9 May 2013
Publication statusPublished - Oct 2013


  • docking
  • MHC class II binding prediction
  • peptide vaccines
  • quantitative matrices


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