How do I retrieve peptides that bind to a specific MHC allele along with their measured IC50 binding affinities?

Originally from ticket #1187.

Question:  How do I retrieve peptides that bind HLA-DRB1*0802 along with their measured IC50 binding affinities?

Answer:  You can perform the query as follows on the IEDB 2.x legacy website:

On the home page search on the left-hand side of the web page, select HLA-DRB1*08:02 in the Allele Finder. Uncheck T cell response, B cell response, and MHC ligand elution, leaving only the MHC binding checked. Click the Search button. On the Search Results Summary, you should see 1130 positive peptidic epitopes and 1170 positive binding assays. Click on the positive binding assay "1170" to get to the MHC binding assay page. You can then download the results in a CSV format by clicking on either the "compact" or "full" next to the Excel icon. Using Excel, you can filter on the "Units" column for IC50 nM. You can then use Excel to remove any duplicates in the Epitope Linear Sequence column.

For the new IEDB 3.0 website, do the following:

On the home page, click on the Search button to get to the first Results page that has the detailed filters on the left-hand side of the page.  In the MHC Restriction box, type the desired allele in the text box to the right of "Specific MHC Restriction."  The text box appears when you mouse over it.  Be sure that "Positive Assays Only" is checked in the Assay box.  Click Search to initiate the new query.  Click on the Assays tab to see all the assays that bound.  Click on the "export epitope results" to download the results and filter on the "Units" column for IC50 nM.  You can then use Excel to remove any duplicates in the Epitope Linear Sequence column.