Computational models for identifying promiscuous HLA-B7 binders based on information theory and support vector machine

Guang Lan Zhang, Joo Chuan Tong, Zong Hong Zhang, Yun Zheng, J. Thomas August, Chee Keong Kwoh, Vladimir Brusic

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Computational vaccinology is a developing discipline. To become a standard component in vaccine development, it requires accurate and broadly applicable models of wet-lab experiments. We developed prediction models based on a novel data representation of peptide/MHC interaction and support vector machines (SVM) for prediction of peptides that promiscuously bind to multiple Human Leukocyte Antigen (HLA) alleles belonging to HLA-B7 supertype. 10-fold cross-validation results showed that the area under the receiver operating curve (Aroc) of SVM models is above 0.90. Blind testing results showed that the average Aroc of SVM models is 0.84. A learning approach based on information theory, termed Information Learning Approach, was used for feature selection. Several amino acid positions with high information content have been identified in input 9mer peptides and HLA alleles and were used as input features to SVM. They are position 1, 2, 4, 5, 7, 8, 9 in 9mer peptides and position 45 and 97 in HLA-B7 molecules. Prediction accuracy was improved after feature selection. These positions cover the anchor positions of HLA-B7 alleles, which have important biological roles for successful biding of relevant peptides.

Original languageEnglish
Title of host publicationICBPE 2006 - Proceedings of the 2006 International Conference on Biomedical and Pharmaceutical Engineering
Pages319-323
Number of pages5
DOIs
Publication statusPublished - Dec 1 2006
EventICBPE 2006 - 2006 International Conference on Biomedical and Pharmaceutical Engineering - Singapore, Singapore
Duration: Dec 11 2006Dec 14 2006

Publication series

NameICBPE 2006 - Proceedings of the 2006 International Conference on Biomedical and Pharmaceutical Engineering

Other

OtherICBPE 2006 - 2006 International Conference on Biomedical and Pharmaceutical Engineering
CountrySingapore
CitySingapore
Period12/11/0612/14/06

Keywords

  • Binding peptide
  • HLA-B7
  • Information thoery
  • Support vector machine
  • Vaccinology

ASJC Scopus subject areas

  • Biomedical Engineering
  • Pharmacology (medical)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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