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BioMed Research International
Volume 2016, Article ID 3832176, 10 pages
Research Article

A Novel Peptide Binding Prediction Approach for HLA-DR Molecule Based on Sequence and Structural Information

1School of Computer Science and Technology, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
2School of Computational Science and Engineering, University of South Carolina, Columbia, SC, USA

Received 10 March 2016; Accepted 4 May 2016

Academic Editor: Yungang Xu

Copyright © 2016 Zhao Li et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


MHC molecule plays a key role in immunology, and the molecule binding reaction with peptide is an important prerequisite for T cell immunity induced. MHC II molecules do not have conserved residues, so they appear as open grooves. As a consequence, this will increase the difficulty in predicting MHC II molecules binding peptides. In this paper, we aim to propose a novel prediction method for MHC II molecules binding peptides. First, we calculate sequence similarity and structural similarity between different MHC II molecules. Then, we reorder pseudosequences according to descending similarity values and use a weight calculation formula to calculate new pocket profiles. Finally, we use three scoring functions to predict binding cores and evaluate the accuracy of prediction to judge performance of each scoring function. In the experiment, we set a parameter in the weight formula. By changing value, we can observe different performances of each scoring function. We compare our method with the best function to some popular prediction methods and ultimately find that our method outperforms them in identifying binding cores of HLA-DR molecules.