IEDB Prediction Tracks
 
Immune Epitope Database and Analysis Resource (IEDB) HLA binding predictions tracks   (All Immunology tracks)

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IEDB Pred Human I  IEDB Epitope Predictions, Human T-Cell Class I  
IEDB Pred Macaque I  IEDB Epitope Predictions, Macaque T-Cell Class I  
IEDB Pred II  IEDB Epitope Predictions, Human T-Cell Class II  
Assembly: Ebola virus Sierra Leone 2014 (G3683/KM034562.1/eboVir3)

Description

The subtracks of this track shows peptides that are predicted to be displayed by human and macaque class I MHCs and human class II MHCs. Class I predictions are split by HLA allele, class II predictions are summarized into a single track.

Display Conventions and Configuration

Class I peptides are shaded by IC50 values and grouped by HLA-alleles. Class II peptides are shaded by percentile.

Methods

Class I T cell epitope prediction: For human epitope prediction, binding affinity for all possible 9-mer peptides from each protein sequence to a set of 27 HLA alleles that are most frequent in the global population, using the SMM method available in the IEDB MHC class I binding prediction tool. All peptides with predicted binding affinity (expressed as IC50 nM) below previously optimized allele-specific thresholds were selected as predicted binders. In the case of rhesus macaque class I T cell epitope prediction, the binding affinity of all 9-mer peptides was predicted for a total of 19 alleles (7 Indian and 12 Chinese rhesus macaques) that are most frequent in these species. The binding affinity predictions utilized the "IEDB recommended" method from the IEDB MHC class I binding prediction tool. Peptides with the IEDB consensus percentile rank <= 1.0 were selected. Lower values for either IC50 or percentile rank indicate stronger binding.

Class II T cell epitope prediction: For human epitope predictions, 15-mer peptides overlapping by 10 aa residues were generated from aligned sequences, to avoid redundant peptides that share the same 9-mer binding core. For each 15-mer peptide, the binding affinity was predicted (expressed as the IEDB consensus percentile rank) for seven class II human HLA alleles (HLA-DRB1*03:01, HLA-DRB1*07:01, HLA-DRB1*15:01, HLA-DRB3*01:01, HLA-DRB3*02:02, HLADRB4*01:01 and HLA-DRB5*01:01), using the IEDB MHC class I binding prediction tool ("IEDB recommended" method). Predicted binders were selected based on the median consensus percentile rank estimated from the consensus percentile ranks for the seven alleles. All peptides with median consensus percentile rank <= 20.0 were selected as predicted binders, the threshold being previously optimized for capturing 50% of class II human T cell responses.