IEDB Analysis Resource

T Cell Epitope Prediction Tools

T Cell Epitopes - MHC Binding Prediction
These tools predict IC50 values for peptides binding to specific MHC molecules. Note that binding to MHC is necessary but not sufficient for recognition by T cells.

Peptide binding to MHC class I molecules ^*
- This tool will take in an amino acid sequence, or set of sequences and determine each subsequence's ability to bind to a specific MHC class I molecule.
Peptide binding to MHC class II molecules
- This tool employs different methods to predict MHC Class II epitopes, including a consensus approach which combines NN-align, SMM-align and Combinatorial library methods.

T Cell Epitopes - Processing Prediction
These tools predict epitope candidates based upon the processing of peptides in the cell.

Proteasomal cleavage/TAP transport/MHC class I combined predictor
- This tool combines predictors of proteasomal processing, TAP transport, and MHC binding to produce an overall score for each peptide's intrinsic potential of being a T cell epitope.
Neural network based prediction of proteasomal cleavage sites (NetChop) and T cell epitopes (NetCTL and NetCTLpan)
- NetChop is a predictor of proteasomal processing based upon a neural network. NetCTL and NetCTLpan are predictors of T cell epitopes along a protein sequence. It also employs a neural network architecture.

^*In addition to these prediction tools, we maintain a separate site for tool developers interested in MHC-I binding predictions. This site contains training and testing data, as well as results from a large scale evaluation of existing prediction tools.

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