Designed CDR clashed with antigen

[wusixer]

Dear author,

5CIL_0023_CDRH3.pdb.zip

I did single cdr loop CDRH3 structure-sequence co-design with input as a pair of Ab-Ag complex and using this exact config file https://github.com/luost26/diffab/blob/main/configs/test/codesign_single.yml. Interestingly, one of the designed loop structure clashed with input antigen. In theory, if the design is conditioned on the antigen structure, we shouldn't observe such clash. Could you please help me understand this specific case?

Thanks!

[xinyangs99]

Hi wusixer, could you elaborate a bit more on your problem? What does the structure clash refer to? Cause I guess I have some similar problems as yours. Thank you!