Issue No. 03 - May-June (2013 vol. 10)
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.78
Stefan Ivanov , Sch. of Pharmacy, Med. Univ. of Sofia, Sofia, Bulgaria
Ivan Dimitrov , Sch. of Pharmacy, Med. Univ. of Sofia, Sofia, Bulgaria
Irini Doytchinova , Sch. of Pharmacy, Med. Univ. of Sofia, Sofia, Bulgaria
The exogenous proteins are processed by the host antigen-processing cells. Peptidic fragments of them are presented on the cell surface bound to the major hystocompatibility complex (MHC) molecules class II and recognized by the CD4+ T lymphocytes. The MHC binding is considered as the crucial prerequisite for T-cell recognition. Only peptides able to form stable complexes with the MHC proteins are recognized by the T-cells. These peptides are known as T-cell epitopes. All T-cell epitopes are MHC binders, but not all MHC binders are T-cell epitopes. The T-cell epitope prediction is one of the main priorities of immunoinformatics. In the present study, three chemometric techniques are combined to derive a model for in silico prediction of peptide binding to the human MHC class II protein HLA-DP1. The structures of a set of known peptide binders are described by amino acid z-descriptors. Data are processed by an iterative self-consisted algorithm using the method of partial least squares, and a quantitative matrix (QM) for peptide binding prediction to HLA-DP1 is derived. The QM is validated by two sets of proteins and showed an average accuracy of 86 percent.
Peptides, Proteins, Immune system, Amino acids, Diseases, Training, Predictive models,partial least squares method, proteins, bonds (chemical), cellular biophysics, least squares approximations, molecular biophysics, quantitative prediction, peptide binding prediction, quantitative matrix, partial least squares, iterative self-consisted algorithm, amino acid z-descriptors, in silico prediction, chemometric techniques, immunoinformatics, MHC binders, T-cell epitopes, MHC proteins, stable complexes, T-cell recognition, MHC binding, CD4+ T lymphocytes, MHC molecules class II, major hystocompatibility complex, cell surface, peptidic fragments, host antigen-processing cells, exogenous proteins, HLA-DP1 protein, Peptides, Proteins, Immune system, Amino acids, Diseases, Training, Predictive models, z-descriptors, MHC binding prediction, iterative self-consistent algorithm
Stefan Ivanov, Ivan Dimitrov, Irini Doytchinova, "Quantitative Prediction of Peptide Binding to HLA-DP1 Protein", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. , pp. 811-815, May-June 2013, doi:10.1109/TCBB.2013.78