IEDB Analysis Resource

Prediction

Analysis

T Cell Epitopes - MHC Binding Prediction
These tools use binding matrices to predict IC50 values for peptides binding to specific MHC molecules.

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 a consensus approach to predict MHC Class II epitopes based upon Sturniolo, ARB, and SMM_align.

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)
- NetChop is a predictor of proteasomal processing based upon a neural network. NetCTL is a predictor of T cell epitopes along a protein sequence. It also employs a neural network architecture.

B Cell Epitope Prediction
The tool here are intended to predict regions of proteins that are likely to be recogized as epitopes in the context of a B cell response.

Prediction of epitopes from protein sequence
- A collection of methods based on amino acid property scales were implemented to predict antigenic determinants or continuous linear B cell epitopes.
Discotope - Prediction of epitopes from protein structure
- This method incorporates solvent-accessible surface area calculations, as well as contact distances into its prediction of B cell epitope potential along the length of a protein sequence.

The epitope analysis tools below are intended for the detailed analysis of a known epitope sequence or group of sequences.

Population Coverage

This tool calculates the fraction of individuals predicted to respond to a given set of epitopes with known MHC restrictions. This calculation is made on the basis of HLA genotypic frequencies assuming non-linkage disequilibrium between HLA loci.

Epitope Conservancy Analysis

This tool calculates the degree of conservancy of an epitope within a given protein sequence set at different degrees of sequence identity. The degree of conservation is defined as the fraction of protein sequences containing the epitope at a given identity level.

Epitope Cluster Analysis

This tool groups epitopes into clusters based on sequence identity. A cluster is defined as a group of sequences which have a sequence similarity greater than the minimum sequence identity threshold specified.

Homology Mapping

This tool maps linear epitopes to 3D structures of proteins. This is done by comparing the epitope source protein sequence with that of proteins with known 3D structures in the PDB. The tool generates an alignment between the query sequence of the epitope source sequence and a homologous sequence from the PDB, and allows to visualize the result in an EpitopeViewer.