Binders were generated using BoltzGen. The number of generations was set to 30,000 with a budget of 100 and an alpha parameter of 0.1 to sample more diverse structures. The nanobody-anything protocol was used. Ten nanobody structures were used as scaffolds for the generation process. They were randomly selected from SAbDab database structures filtered by resolution (less than 1.5 Å) while maintaining the diversity of CDR lengths. All three CDRs were redesigned during generation. The target structure was also provided in the generation pipeline. Amino acids in contact with zinc ions were restricted for binding; the structure of the disordered tail of RBX1 was not specified.

After generation, an additional refolding filter (AlphaFold2) was used to check the consistency of the generated and predicted structures. Then designs were filtered by criteria of binding to the RBX1 ordered part and lack of interactions with zinc ions and with RBX1 residues in contact with zinc ions.

Listed filtration steps were passed by 3 designs, which are ranked as top 3 in current submission. Other designs ranked according to their success in passing the filters and to the results of manual structural analysis.