MHC class II binding predictions

This program was written by Ilan Volovitz working in Lea Eisenbach's lab in the Weizmann Institute of Science.
For a copy of a draft manuscript which describes the algorithm, please contact the author.

This program receives a protein sequence and determines which of all possible nonamers bind to a specific MHC class II molecule. Each window of nine amino acids is compared to a known motif in an affinity of binding determined by the user.


Paste protein sequence here:

Select which MHC class II motif you would like the program to use.


For which kind of binders should the search be?
(please note that in all DRB molecules only one kind of motif was entered for high, medium or low affinities)

Exact motif fitting-(highest binders)
Medium to high binders
Low to high binding affinities (lowest stringency search)