tooluniverse-hla-immunogenomics

Search IEDB for the target MHC allele using its full nomenclature (e.g., HLA-A*02:01) to retrieve experimentally measured binding data. Results include IC50 values, where under 500 nM typically indicates a class I binder.

Query IEDB by organism name and source antigen to get experimentally validated epitopes with MHC restriction and assay results. BVBRC can supplement with additional pathogen-derived epitopes including host MHC context.

No. It queries experimental databases like IEDB, not prediction algorithms such as NetMHCpan or MHCflurry. Absence of an epitope in IEDB means it has not been tested, not that it cannot bind.

Class I molecules (HLA-A, B, C) present 8-11 amino acid peptides to CD8+ T cells, while class II molecules (HLA-DR, DQ, DP) present 13-25 amino acid peptides to CD4+ T cells. Class II binding data is less mature because the molecules are heterodimers.

Well-known associations include HLA-B*57:01 with abacavir, HLA-B*15:02 with carbamazepine in Southeast Asian populations, and HLA-B*58:01 with allopurinol. The Skill verifies these against DGIdb and PubMed rather than relying on memory.

IEDB coverage is biased toward well-studied pathogens like HIV, influenza, and SARS-CoV-2 and common HLA alleles. For broad population coverage, select epitopes across multiple HLA supertypes such as A2, A3, B7, and B44.