Campus Units

Genetics, Development and Cell Biology, Bioinformatics and Computational Biology, Computer Science

Document Type

Article

Publication Version

Accepted Manuscript

Publication Date

2011

Journal or Book Title

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volume

8

Issue

4

First Page

1067

Last Page

1079

DOI

10.1109/TCBB.2010.94

Abstract

Reliably predicting the ability of antigen peptides to bind to major histocompatibility complex class II (MHC-II) molecules is an essential step in developing new vaccines. Uncovering the amino acid sequence correlates of the binding affinity of MHC-II binding peptides is important for understanding pathogenesis and immune response. The task of predicting MHC-II binding peptides is complicated by the significant variability in their length. Most existing computational methods for predicting MHC-II binding peptides focus on identifying a nine amino acids core region in each binding peptide. We formulate the problems of qualitatively and quantitatively predicting flexible length MHC-II peptides as multiple instance learning and multiple instance regression problems, respectively. Based on this formulation, we introduce MHCMIR, a novel method for predicting MHC-II binding affinity using multiple instance regression. We present results of experiments using several benchmark datasets that show that MHCMIR is competitive with the state-of-the-art methods for predicting MHC-II binding peptides. An online web server that implements the MHCMIR method for MHC-II binding affinity prediction is freely accessible at http://ailab.cs.iastate.edu/mhcmir.

Comments

This article is from IEEE/ACM Transactions on Computational Biology and Bioinformatics 8 (2011): 1067, doi: 10.1109/TCBB.2010.94. Posted with permission.

Rights

© 2011 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.

Copyright Owner

IEEE

Language

en

File Format

application/pdf

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