Gibbs Motif Sampler, Weight Matrix and Artificial Neural Network for the Prediction of MHC Class-II Binding Peptides

  • Satarudra Prakash Singh
  • Bhartendu Nath Mishra
Conference paper

DOI: 10.1007/978-3-642-03547-0_48

Part of the Communications in Computer and Information Science book series (CCIS, volume 40)
Cite this paper as:
Singh S.P., Mishra B.N. (2009) Gibbs Motif Sampler, Weight Matrix and Artificial Neural Network for the Prediction of MHC Class-II Binding Peptides. In: Ranka S. et al. (eds) Contemporary Computing. IC3 2009. Communications in Computer and Information Science, vol 40. Springer, Berlin, Heidelberg

Abstract

The identification of MHC class-II restricted epitope is an important goal in peptide based vaccine and diagnostic development. In the present study, we discuss the applications of Gibbs motif sampler, weight matrix and artificial neural network for the prediction of peptide binding to sixteen MHC class-II molecules of human and mouse. The average prediction performances of sixteen MHC class-II molecules in terms of Aroc, based on Gibbs motif sampler, sequence weighting and artificial neural network are 0.56, 0.55 and 0.51 respectively. However, further improvements in the performance of software tools for prediction of MHC class-II binding peptide based on various methods largely depends on the size of training and validation datasets and the correct identification of the peptide binding core.

Keywords

MHC Weight matrix ANN Gibbs sampler Motif Epitope 

Abbreviations

ANN-artificial neural network MHC-major histocompatibility complex Aroc-area under receiver operating characteristic IEDB- immune epitope database 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Satarudra Prakash Singh
    • 1
    • 2
  • Bhartendu Nath Mishra
    • 2
  1. 1.Amity Institute of BiotechnologyAmity University Uttar PradeshLucknowIndia
  2. 2.Department of Biotechnology, Institute of Engineering & TechnologyU.P. Technical UniversityLucknowIndia

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