Prediction of MHC-binding peptides of flexible lengths from sequence-derived structural and physicochemical properties

J. Cui, L. Y. Han, H. H. Lin, H. L. Zhang, Z. Q. Tang, C. J. Zheng, Z. W. Cao, Y. Z. Chen

Research output: Contribution to journalArticlepeer-review

58 Scopus citations


Peptide binding to MHC is critical for antigen recognition by T-cells. To facilitate vaccine design, computational methods have been developed for predicting MHC-binding peptides, which achieve impressive prediction accuracies of 70-90% for binders and 40-80% for non-binders. These methods have been developed for peptides of fixed lengths, for a limited number of alleles, trained from small number of non-binders, and in some cases based straightforwardly on sequence. These limit prediction coverage and accuracy particularly for non-binders. It is desirable to explore methods that predict binders of flexible lengths from sequence-derived physicochemical properties and trained from diverse sets of non-binders. This work explores support vector machines (SVM) as such a method for developing prediction systems of 18 MHC class I and 12 class II alleles by using 4208-3252 binders and 234,333-168,793 non-binders, and evaluated by an independent set of 545-476 binders and 110,564-84,430 non-binders. Binder accuracies are 86-99% for 25 and 70-80% for 5 alleles, non-binder accuracies are 96-99% for 30 alleles. Binder accuracies are comparable and non-binder accuracies substantially improved against other results. Our method correctly predicts 73.3% of the 15 newly-published epitopes in the last 4 months of 2005. Of the 251 recently-published HLA-A*0201 non-epitopes predicted as binders by other methods, 63 are predicted as binders by our method. Screening of HIV-1 genome shows that, compared to other methods, a comparable percentage (75-100%) of its known epitopes is correctly predicted, while a lower percentage (0.01-5% for 24 and 5-8% for 6 alleles) of its constituent peptides are predicted as binders. Our software can be accessed at

Original languageEnglish (US)
Pages (from-to)866-877
Number of pages12
JournalMolecular Immunology
Issue number5
StatePublished - Feb 2007
Externally publishedYes


  • Epitopes
  • MHC binding peptide
  • SVM
  • Vaccine

ASJC Scopus subject areas

  • Immunology
  • Molecular Biology


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