Use case two: Predicting anibody epitopes
Problem
We would like to assess whether AlphaFold3 can predict antibody epitopes. We use SabDab to collect structures. We use AlphaFold3 server to predict the structures.
Initial dataset
We have a list of PDB chain pairs containing antibody-antigene interactions.
?
We run AlphaFold-multimer in template mode on sequences from PDB structures. How to construct our benchmark set?
!
Use interacting chains with a date after your template library cutoff.
Proposed protocol with BETA
- According to the FAQ provided to AlphaFold3 the server does not use structures submitted to PDB after 30.09.2021.
- Go to the BETA download. On the navbar above type your PDB code into the search input field, then select the closest date after training and template library release, that is 01.10.2021.
- The intersection of the original benchmark set (step 1) and the filtered set from BETA (step 2) should be used to evaluate predictions.