User:Immunos/Epitope prediction

Epitope prediction is a key problem in computational immunology. An epitope is a part of an antigen that is recognized by the immune system. One distinguishes between B-cell and T-cell epitopes. Epitope prediction helps to gain a deeper understanding of immune responses and is of great interest to vaccine design.

T-Cell Epitope Prediction
T-cell epitopes are peptides derived from antigenic proteins that are presented on the cell surface by MHC molecules and recognized by T cells. Due to the highly complex and so far not sufficiently understood processes governing T-cell response, prediction of T-cell epitopes is a very challenging problem. Available prediction methods are not sufficiently accurate to be beneficial for vaccine design.

MHC-peptide binding on the other hand can be accurately predicted. Since it is essential, albeit not sufficient, for a T-cell epitope to bind to an MHC molecule, MHC-binding prediction is commonly used as an alternative to epitope prediction. Often, the term Epitope prediction actually refers to MHC-binding prediction.

A wide variety of methods have been proposed to predict MHC-binding peptides.

MHC class I binding prediction can be improved by additionally predicting the antigen processing pathway, namely the degradation of the protein by the proteasome, and the transport of peptides from the cytosol into the endoplasmatic reticulum by TAP. Peptides that bind to MHC but are not produced by the antigen processing machinery are filtered out. There exist methods for proteasomal cleavage and TAP transport alone. Some integrated methods for the prediction of antigen processing and MHC binding have also been published.

The prediction of T-cell reactivity of peptide:MHC complexes has also been addressed computationally. These attempts are only moderately successful.

B-Cell Epitope Prediction
While T-cell epitopes are linear epitopes, B-cell epitopes (structures that are recognized by B-cell receptors or antibodies) are mostly conformational epitopes, i.e. they exist within the tertiary structure of the antigen. The prediction of B-cell epitopes has therefore been less successful than the prediction of T-cell epitopes.

T-Cell Epitope Prediction

 * NetMHC
 * NetMHCpan
 * SYFPEITHI
 * BIMAS/HLA-Bind
 * SVMHC
 * WAPP
 * NetCTL

Interfaces to Multiple Prediction Methods

 * EpiToolKit
 * immuneepitope.org/IEDB

T-cell Reactivity Prediction

 * POPI

B-Cell Epitope Prediction

 * DiscoTope
 * BepiPred
 * Epitopia