Computational protocol: Homology modeling and epitope prediction of Der f 33

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Protocol publication

[…] Der f 33 amino acid sequence (Accession Number: AIO08861.1) was obtained from the International Union of Immunological Societies (IUIS) nomenclature database and the protein database of National Center for Biotechnology Information (NCBI). Family classification of Der f 33 was analyzed by Superfamily v1.75 () and InterPro v56.0 (). TMHMM server 2.0 () was used for predicting the transmembrane helices in Der f 33 proteins. [...] ABCpred (), BCPreds (), BcePred (), and Bioinformatics Predicted Antigenic Peptides (BPAP) system () were used for predicting B cell epitopes of Der f 33. ABCpred predicted B cell epitopes in antigen sequences, using an artificial neural network. BCPreds selected AAP method (), BCPred (), and FBCPred () to predict B cell epitopes. BcePred and BPAP system predicted B cell epitopes using the same physicochemical properties, such as hydrophilicity, flexibility/mobility, accessibility, polarity, exposed surface, and turns. [...] T cell epitopes were predicted by identifying the binding of peptides to MHC molecules with NetMHCII 2.2 () and NetMHCIIpan-3.1 ().NetMHCII 2.2 uses artificial neuron networks to predict binding of epitope peptides to HLA-DQ alleles in regions of HLA-DQA10101-DQB10501, HLA-DQA10102-DQB10602, HLA-DQA10301-DQB10302, HLA-DQA10401-DQB10402, HLA-DQA10501-DQB10201, and HLA-DQA10501-DQB10301.NetMHCIIpan-3.1 was used for HLA-DR-based epitope prediction in regions of HLA-DR DRB101, HLA-DRB301, HLA-DRB401, and HLA-DRB501.In the 2 programs, high binding peptides have an IC50 value below 50 nM. The ultimate T cell epitopes were obtained by combining the results of the HLA-DR alleles epitopes and HLA-DQ alleles epitopes. […]

Pipeline specifications

Software tools ABCpred, BCPREDS, Bcepred, NetMHCIIpan
Application Immune system analysis
Organisms Dermatophagoides farinae
Chemicals Amino Acids