MULTIPRED2: a system for large-scale screening of allele-, genotype-, and supertype-specific HLA associated peptides

MULTIPRED2 is a computational system for large-scale screening of peptide binding to multiple alleles belonging to human leukocyte antigen (HLA) class I and class II DR supertypes as well as to alleles belonging to an individual's genotype. netMHCpan and netMHCIIpan are used as prediction engines. In total MULTIPRED2 performs binding predictions on 1077 alleles belonging to 26 HLA supertypes. Built upon our previous developments - MULTIPRED and PEPVAC, MULTIPRED2 is for mapping of promiscuous T-cell epitopes as well as the regions of high concentration of these targets - termed T-cell epitope hotspots.

Class I supertypes:
A1, A2, A3, A24, A26, B7, B8, B27, B44, B58, B62, C1, and C4
Class II supertypes:
DR1, DR3, DR4, DR6, DR7, DR8, DR9, DR11, DR12, DR13, DR14, DR15, and DR16

If you are interested in performing prediction on a large amount of data, for example a whole viral proteome, you can send the protein sequences to and we will perform prediction, post the results online, and send you the result URL. For details of the system, please refer to the papers below:

Zhang GL, Deluca DS, Keskin DB, Chitkushev L, Zlateva T, Lund O, Reinherz EL, Brusic V.(2011) MULTIPRED2: A computational system for large-scale identification of peptides predicted to bind to HLA supertypes and alleles. J Immunol Methods.

Latest update on July 22nd, 2014 - updated the system to use the latest version of prediction servers: NetMHCpan 2.8a and NetMHCIIpan 3.0.
Version 1.0, Feburary 2010. Developed by Bioinformatics Core at Cancer Vaccine Center, Dana-Farber Cancer Institute.