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The WAPP prediction server

WAPP is a prediction server for the Whole Antigen Processing Pathway of MHC class I molecules. The main events in the processing pathway are Proteosomal cleavage, TAP transport, and MHC-peptide binding. WAPP offers an integrated prediction for these three steps.

How to cite the prediction service

Integrated modelling of the major events in the MHC class I antigen processing pathway", Dönnes, P and Kohlbacher, O, Protein Science, 2005, 14(8):2132-40

Input format

There are two ways to submit data for prediction: Sequences can be pasted into the input field directly in FASTA format or database IDs can be specified. In the case of database ids, both, SWISSPROT accession numbers (e.g. P18146 or EGR1_HUMAN) and NCBI RefSeq accession numbers(e.g. NP_055147) can be used. These sequences will then be retrieved from a local copy of these databases.

Cutoff values

After initial prediction, the parameters used for each individual method can be tuned. For each method a level from 0 to 5 can be chosen. The value 0 will turn that prediction off, meaning that all peptides will pass this step. Increasing the cutoff give less peptides.

Prediction methods

Proteasomal cleavage

Prediction of Proteasomal cleavage is based on experiments done on the Enolase and Prion proteins.
Sequences around experimental cleavage sites were extracted and a weight matrix constructed.

TAP transport

A regression form of Support Vector Machines (SVMs) is used for prediction of TAP affinity. The data
used for training consists of experimentally verified binding affinities (IC50)for peptides to TAP.

MHC-peptide binding

The method used for prediction of MHC-peptide binding is SVMHC. For detail see:
Prediction of MHC class I binding peptides, using SVMHC. Dönnes and Elofsson in: BMC Bioinformatics 2002 3: 25.