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Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications

Academic Article
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Overview

authors

  • Bui, H. H.
  • Sidney, J.
  • Peters, B.
  • Sathiamurthy, M.
  • Sinichi, A.
  • Purton, K. A.
  • Mothe, B. R.
  • Chisari, Francis
  • Watkins, D. I.
  • Sette, Alessandro

publication date

  • June 2005

journal

  • Immunogenetics  Journal

abstract

  • Prediction of which peptides can bind major histocompatibility complex (MHC) molecules is commonly used to assist in the identification of T cell epitopes. However, because of the large numbers of different MHC molecules of interest, each associated with different predictive tools, tool generation and evaluation can be a very resource intensive task. A methodology commonly used to predict MHC binding affinity is the matrix or linear coefficients method. Herein, we described Average Relative Binding (ARB) matrix methods that directly predict IC(50) values allowing combination of searches involving different peptide sizes and alleles into a single global prediction. A computer program was developed to automate the generation and evaluation of ARB predictive tools. Using an in-house MHC binding database, we generated a total of 85 and 13 MHC class I and class II matrices, respectively. Results from the automated evaluation of tool efficiency are presented. We anticipate that this automation framework will be generally applicable to the generation and evaluation of large numbers of MHC predictive methods and tools, and will be of value to centralize and rationalize the process of evaluation of MHC predictions. MHC binding predictions based on ARB matrices were made available at http://epitope.liai.org:8080/matrix web server.

subject areas

  • Animals
  • Binding Sites
  • Computer Simulation
  • Databases, Protein
  • Epitopes
  • Histocompatibility Antigens
  • Humans
  • Major Histocompatibility Complex
  • Models, Biological
  • Protein Binding
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Research

keywords

  • MHC
  • Web server
  • automated tool evaluation
  • binding prediction
  • computer algorithms
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Identity

International Standard Serial Number (ISSN)

  • 0093-7711

Digital Object Identifier (DOI)

  • 10.1007/s00251-005-0798-y

PubMed ID

  • 15868141
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Additional Document Info

start page

  • 304

end page

  • 314

volume

  • 57

issue

  • 5

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