MHC binding prediction with KernelRLSpan and its variations

Wen Jun Shen, Yu Ting Wei, Xin Guo, Stephen Smale, Hau San Wong, Shuai Cheng Li

Research output: Journal article publicationJournal articleAcademic researchpeer-review

8 Citations (Scopus)

Abstract

Antigenic peptides presented to T cells by MHC molecules are essential for T or B cells to proliferate and eventually differentiate into effector cells or memory cells. MHC binding prediction is an active research area. Reliable predictors are demanded to identify potential vaccine candidates. The recent kernel-based algorithm KernelRLSpan (Shen et al., 2013) shows promising power on MHC II binding prediction. Here, KernelRLSpan is modified and applied to MHC I binding prediction, which we refer to as KernelRLSpanI. Besides this, we develop a novel consensus method to predict naturally processed peptides through integrating KernelRLSpanI with two state-of-the-art predictors NetMHCpan and NetMHC. The consensus method achieved top performance in the Machine Learning in Immunology (MLI) 2012 Competition,.33URL: http://bio.dfci.harvard.edu/DFRMLI/HTML/natural.php. group 2. We also introduce our progress of improving our MHC II binding prediction method KernelRLSpan by diffusion map.
Original languageEnglish
Pages (from-to)10-20
Number of pages11
JournalJournal of Immunological Methods
Volume406
DOIs
Publication statusPublished - 1 Jan 2014
Externally publishedYes

Keywords

  • Diffusion map
  • Eluted peptide prediction
  • Major histocompatibility complex class I
  • Major histocompatibility complex class II
  • MHC
  • Peptide binding prediction
  • String kernel

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology

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