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A novel representation of HLA allele specificity and prediction algorithm for HLA class I binding

Published: 02 August 2010 Publication History

Abstract

Current software tools and algorithms for prediction of HLA class I peptide binding prediction are based on the frequency of 2 anchoring residues from peptides of 8 to 9 residues long with less account for variable peptide length or amino acid residues internal to anchor positions. We herein propose an algorithm based on data obtained by mass spectrometric sequencing of eluted peptides using amino acid properties of key peptide anchor position residues and internal residues between anchor positions.

References

[1]
Rammensee, H. G., T. Friede, and S. Stevanoviic, MHC ligands and peptide motifs: first listing. Immunogenetics, 1995. 41(4): p. 178--228.
[2]
Robinson, J., et al., IMGT/HLA database--a sequence database for the human major histocompatibility complex. Tissue Antigens, 2000. 55(3): p. 280--7.
[3]
Peters, B., et al., The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol, 2005. 3(3): p. e91.
[4]
Escobar, H., et al., Large scale mass spectrometric profiling of peptides eluted from HLA molecules reveals N-terminal-extended peptide motifs. J Immunol, 2008. 181(7): p. 4874--82.
[5]
Kawashima, S. and M. Kanehisa, AAindex: amino acid index database. Nucleic Acids Res, 2000. 28(1): p. 374.
[6]
Hall, M. A., Correlation-based feature selection of discrete and numeric class machine learning, in Computer Science Working Papers. 2000, University of Waikato, Department of Computer Science: Hamilton, New Zealand.
[7]
Witten and Frank. Data Mining: Practical machine learning tools and techniques. 2nd edition ed. 2005, San Francisco: Morgan Kaufmann.

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  1. A novel representation of HLA allele specificity and prediction algorithm for HLA class I binding

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    cover image ACM Conferences
    BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
    August 2010
    705 pages
    ISBN:9781450304382
    DOI:10.1145/1854776
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    Published: 02 August 2010

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    Author Tags

    1. HLA allele
    2. binding prediction
    3. classification
    4. machine learning

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