MHC & Algorithm

Major Histocompatibility Complex molecules are cell surface glycoproteins that play a crucial role in initiating and regulating immune response. MHC binds peptides within the cell and presents them at the cell surface for interaction with T-Cells as a part of the immune system's mechanisms for identifying and responding to foreign antigens. Binding of a peptide to a MHC molecule is prerequisite for recognition by the T-cells.
X-ray structure has revealed that peptide binding groove of MHC class II molecules is open at both ends. A binder may flank from on or other side of groove.

Understanding which residues are involved in interaction with MHC molecules will provide an understanding mechanisms of binding or more specifically permissive binding anchors. It will also help to devlop better MHC binding peptide prediction methods.

Present developed methods to predict binding core relies on the discrimination between binders and nonbinders.The thought behind these methods is that binding core has motifs which can be distinguished  from nonbinders. In this trend an accuracy of more than 90% has been reported for HLA-DR1 allele.

The method used in this server is simple and effective. It uses iterations to optimize every element of matrix. These iterations finally produce a matrix with highest discriminating capability. The method has produced matrix with 97 to 99% accuracy on HLA-DR1, HLA-DR2 and HLA-DR5 alleles.
Server takes your antigen sequence as input and search for any binding motif or core in that. These motifs will be predicted by server as potential binders.

Hope you find it educative and useful.