MHCPred uses the additive method to predict the binding affinity of major histocompatibility complex (MHC) class I and II molecules and also to the Transporter associated with Processing (TAP). Allele specific Quantitative Structure Activity Relationship (QSAR) models were generated using partial least squares (PLS).

How to use the query form:


Sequences are limited to a maximum of 1000 residues. Longer sequences are not be accepted, for reasons of CPU usage, so please check before submitting. Currently only sequences in plain format are accepted: other formats, such as FASTA or GCG, are not accepted by MHCPred.

Select the allele:

Class I MHC Class II MHC Other
HLA_A*0101 DRB1*0101 TAP
HLA_A*0201 DRB1*0401  
HLA_A*0202 DRB1*0701  

Select the model:

Two models are used for binding affinity prediction. The first uses only amino acids contribution; the second is based on the contributions of amino acids and their interactions.

The cut-off value of IC50:

Suggested IC50 values are between 0.01 to 5000 nM. If the value is above 5000, then the peptide is unlikely to bind MHC molecules. 

Select the anchor positions:

The user can select specific residues at specific anchor positions. The maximum number of selected anchor positions is 4.
Note: The positions have to be different each time, i.e. the user cannot enter the same position twice.


The results of the program is shown in a table with three columns. The first column shows the peptide sequences, the second and the third column show the predicted IC50 and IC50 values respectively. If the IC50 value is above 5000 then the peptide will not bind to the MHC molecules. The order of the peptides is sorted by the IC50 values. Peptides with lower IC50 values (or higher predicted IC50 value) are listed first, and the non-binders are listed at the bottom of the table. To view the position of an interested peptide, the user can click on the peptide and the query sequence will be shown in a separate window, with the peptide in question highlighted.


nM = 10-9 M. Molar is traditionally used by chemists to describe the concentration of chemical solutions. "molar" describes a concentration in moles per liter (mol/L). A solution described as 1.0 ÁM has a concentration of 1.0 Ámol/L. Mole is the SI fundamental unit of the amount of a substance (as distinct from its mass or weight). Moles measure the actual number of atoms or molecules in an object. The official definition, adopted as part of the SI system in 1971, is that one mole of a substance contains just as many elementary entities (atoms, molecules, ions, or other kinds of particles) as there are atoms in 12 grams of carbon 12. The actual number of "elementary entities" in a mole is called Avogadro's number after the Italian chemist and physicist Amedeo Avogadro (1776-1856). Careful measurement determines Avogadro's number to be approximately 602.214 199 x 1021 entities per mole.