Mutation in epitope sequence and HLA binding preference

Question

[rajmandage]

I have 500 epitope sequences with the list of mutations in the epitope sequences. In the following example, I have observed mutation at 3rd potion where G is replaced by R. I would like to study the impact of this mutation on the HLA allele recognition and binding preference by respective epitope. Whether the replacement of G by R alters the recognition of HLA-A3 or still it recognizes HLA-A3?

There are few bioinformatics tools are available to study this binding interaction using PDB files. However, I don't have 3D structure (PDB files ) of antigen (epitope seq) to go with the structural bioinformatics approach. Is there any sequence-based approach available to check binding preference?

Epitope Seq . Mutation HLA Allele Reconisation GDGAAGQPA No mutation HLA-A3 GDRAAGQPA 3GR (mutation at 3rd postion) HLA-A3 (??)

Answer 1

[igor]

If I understand correctly, you want to check the binding strength based on the peptide sequence. There are a few different tools that can do that. Probably the most famous is NetMHC.

There is a recent review (Zhao and Sher) that lists many of them: