PAAQD: Predicting immunogenicity of MHC class I binding peptides using amino acid pairwise contact potentials and quantum topological molecular similarity descriptors.
Prediction of peptide immunogenicity is a promising approach for novel vaccine discovery. Conventionally, epitope prediction methods have been developed to accelerate the process of vaccine production by searching for candidate peptides from pathogenic proteins. However, recent studies revealed that peptides with high binding affinity to major histocompatibility complex molecules (MHCs) do not always result in high immunogenicity. Therefore, it is promising to predict the peptide immunogenicity rather than epitopes in order to discover new vaccines more effectively. To this end, we developed a novel T-cell reactivity predictor which we call PAAQD. Nonapeptides were encoded numerically, using combining information of amino acid pairwise contact potentials (AAPPs) and quantum topological molecular similarity (QTMS) descriptors. Encoded data were used in the construction of our classification model. Our numerical experiments suggested that the predictive performance of PAAQD is at least comparable with POPISK, one of the pioneering techniques for T-cell reactivity prediction. Also, our experiment suggested that the first and eighth positions of nonapeptides are the most important for immunogenicity and most of the anchor residues in epitope prediction were not important in T-cell reactivity prediction. The R implementation of PAAQD is available at http://pirun.ku.ac.th/~fsciiok/PAAQD.rar.
Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan. thammakorn.kmutt@gmail.com
Thammakorn
T
Saethang
Osamu
O
Hirose
Ingorn
I
Kimkong
Vu Anh
VA
Tran
Xuan Tho
XT
Dang
Lan Anh T
LA
Nguyen
Tu Kien T
TK
Le
Mamoru
M
Kubo
Yoichi
Y
Yamada
Kenji
K
Satou
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000276:immunology* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D018984:Epitopes, T-Lymphocyte / Q000276:immunology / Q000378:metabolism; D015395:Histocompatibility Antigens Class I / Q000276:immunology* / Q000378:metabolism; D020407:Internet; D009842:Oligopeptides / Q000276:immunology* / Q000378:metabolism; D011485:Protein Binding / Q000276:immunology; D015203:Reproducibility of Results; D013601:T-Lymphocytes / Q000276:immunology / Q000378:metabolism
D000596:Amino Acids; D018984:Epitopes, T-Lymphocyte; D015395:Histocompatibility Antigens Class I; C408902:MHC binding peptide; D009842:Oligopeptides