chain scission on antigen

[yangly-simon]

I'm wondering why there are chain breaks on the antigen when designing an antibody for PDL-1?
What factors may cause this?

[xgqaikgh]

This issue is likely caused by the fact that the antigen PDB you provided contains discontinuous atoms/residues. When I initially prepared the antigen input file, I selected only the spatially proximal residues within the RBD to serve as the antibody.target_pdb, in order to speed up the design process. Although this approach significantly reduced runtime, it resulted in chain discontinuities.

Upon further consideration, I realized that this strategy was not sufficiently rigorous, as it could allow the antibody to bind to antigen sites that are not actually exposed in the native structure. Therefore, I reran the calculations using a continuous antigen sequence instead.