PREDBALB/c: a system for the prediction of peptide binding to H2d molecules, a haplotype of the BALB/c mouse

Abstract

PRED(BALB/c) is a computational system that predicts peptides binding to the major histocompatibility complex-2 (H2(d)) of the BALB/c mouse, an important laboratory model organism. The predictions include the complete set of H2(d) class I (H2-K(d), H2-L(d) and H2-D(d)) and class II (I-E(d) and I-A(d)) molecules. The prediction system utilizes quantitative matrices, which were rigorously validated using experimentally determined binders and non-binders and also by in vivo studies using viral proteins. The prediction performance of PRED(BALB/c) is of very high accuracy. To our knowledge, this is the first online server for the prediction of peptides binding to a complete set of major histocompatibility complex molecules in a model organism (H2(d) haplotype). PRED(BALB/c) is available at http://antigen.i2r.a-star.edu.sg/predBalbc/.

Figure 1

An example of the output pages of PRED^BALB/c when the input is a single protein. The input protein sequence is Staphylococcal nuclease (Nase), the sequence type chosen is ‘protein sequence’ and the H2^d alleles of interest are all H2^d alleles. (A) The input page. (B) The main result page. The input sequence is decomposed into overlapping 9mers for the prediction of binding scores to each allele. (C) Graphical view of the predicted binding scores to the I-E^d molecule.

Figure 2

An example of the output pages of PRED^BALB/c when the input is a list of peptides. The input is a list of peptides from chicken ovalbumin and the H2^d alleles of interest are all H2^d alleles. (A) The input page. (B) The main result page. All 9mers in each peptide are submitted for prediction. The predicted binding scores are represented by the highest individual 9mer binding score of each input peptide. (C) The alignment view of the predicted binding peptides at threshold 9, which indicates that the specificity of the prediction is 0.9.