Matrix Optimization Technique for Predicting MHC binding Core

The X-ray crystal structure of MHC class II molecule has revealed open peptide binding groove. A peptide bound in this groove may flank from one or the other side. Understanding which residues are acctually involved in binding will be very useful for understanding MHC peptide interactios. We have used Matrix Optimization Technique to predict MHC binding core. Using binders from MHCPEP and nonbinder Data with MOT an accuracy of correct classification from 97 to 99% was obtained with HLA-DR1, HLA-DR2 and HLA-DR5 allele. This is the highest accuracy reported by any method. The prediction method used in this server is based on MOT and relies on the thought that binders have unique patterns which can be easily distinguished from nonbinders.
The web based server linked here predict MHC binding regions/motifs in given antigen sequence. Example Results

Developed By

Harpreet Singh and G P S Raghava
Bioinformatics Centre
Institute of Microbial Technology,
Sector 39A, Chandigarh,
India 

Contact Address

Email: raghava@imtech.ernet.in
Internet: http://imtech.ernet.in/raghava
Phone: +91-172-690557,+91-172-690908
Fax: +91-172-690632,+91-172-690585