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Quantitative modeling of peptide binding to TAP using support vector machine

Diez Rivero, Carmen and Chenlo, Bernardo and Zuluaga Arias, Pilar and Reche, Pedro A (2010) Quantitative modeling of peptide binding to TAP using support vector machine. Proteins, 78 (1). pp. 63-72. ISSN 1097-0134

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Official URL: http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0134

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Abstract

The transport of peptides to the endoplasmic reticulum by the transporter associated with antigen processing (TAP) is a necessary step towards determining CD8 T cell epitopes. In this work, we have studied the predictive performance of support vector machine models trained on single residue positions and residue combinations drawn from a large dataset consisting of 613 nonamer peptides of known affinity to TAP. Predictive performance of these TAP affinity models was evaluated under 10-fold cross-validation experiments and measured using Pearson's correlation coefficients (R(p)). Our results show that every peptide position (P1-P9) contributes to TAP binding (minimum R(p) of 0.26 +/- 0.11 was achieved by a model trained on the P6 residue), although the largest contributions to binding correspond to the C-terminal end (R(p) = 0.68 +/- 0.06) and the P1 (R(p) = 0.51 +/- 0.09) and P2 (0.57 +/- 0.08) residues of the peptide. Training the models on additional peptide residues generally improved their predictive performance and a maximum correlation (R(p) = 0.89 +/- 0.03) was achieved by a model trained on the full-length sequences or a residue selection consisting of the first 5 N- and last 3 C-terminal residues of the peptides included in the training set. A system for predicting the binding affinity of peptides to TAP using the methods described here is readily available for free public use at http://imed.med.ucm.es/Tools/tapreg/.


Item Type:Article
Uncontrolled Keywords:Antigen processing; Peptide; TAP; Prediction; WEKA; SVM
Subjects:Medical sciences > Medicine > Immunology
Sciences > Computer science > Bioinformatics
ID Code:11335
Deposited On:20 Oct 2010 14:20
Last Modified:20 Oct 2010 14:21

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