BoltzGen was employed to design peptides/small proteins (40 to 80 residues) to bind the disordered region of RBX1 (I wanted to check how BoltzGen can be used for this kind of target which is usually not easy to deal with). The detailed method/settings is described in the "Design method" field in the submission.

The most interesting part of the submission is the top 8 sequences, which were selected by refolding the best BoltzGen-generated sequences (see BoltzGen + AFmm refolding with ipTM and contact analysis Design Method) with AlphaFold-Multimer, then applying an ipTM cutoff and a minimum of 25% of residues in the disordered region of RBX1 (residues 1-32) involved in an interaction with the candidate. The first candidate in the submission forms 16 contacts in this region in the best AFmm model, where a segment of the initially disordered region adopts a beta-sheet conformation. This segment inserts between beta-strands of the binder.

Outside the top 8 candidates, the sequences designed by BoltzGen are simply ranked based on the vanilla scoring function (see BoltzGen Design Method)