Running a docked antigen-antibody structure

[PCRandChill]

Hi Kevin,

Thank you for providing an excellent project. I wanted to test it out on structures docked using HADDOCK. The CAPRI scores for the top model show that it is a high-quality model. I wanted to identify the binding affinity using ANTIPASITY. I tried using your tutorial, but I'm not following why these structures below are selected and if I should be changing them. Could you elaborate on this step? Thank you!

pathological = ['5omm', '5i5k', '1uwx', '1mj7', '1qfw', '1qyg', '4ffz', '3ifl', '3lrh', '3pp4', '3ru8', '3t0w', '3t0x', '4fqr', '4gxu', '4jfx', '4k3h', '4jfz', '4jg0', '4jg1', '4jn2', '4o4y', '4qxt', '4r3s', '4w6y', '4w6y', '5ies', '5ivn', '5j57', '5kvd', '5kzp', '5mes', '5nmv', '5sy8', '5t29', '5t5b', '5vag', '3etb', '3gkz', '3uze', '3uzq', '4f9l', '4gqp', '4r2g', '5c6t', '3fku', '1oau', '1oay']
scfv = ['4gqp', '3etb', '3gkz', '3uze', '3uzq', '3gm0', '4f9l', '6ejg', '6ejm', '1h8s', '5dfw', '6cbp', '4f9p', '5kov', '1dzb', '5j74', '5aaw', '3uzv', '5aam', '3ux9', '5a2j', '5a2k', '5a2i', '3fku', '5yy4', '3uyp', '5jyl', '1y0l', '1p4b', '3kdm', '4lar', '4ffy', '2ybr', '1mfa', '5xj3', '5xj4', '4kv5', '5vyf']

[kevinmicha]

Hi,

Those structures are considered pathological because they may have missing amino acids or fail to meet any of the filtering criteria mentioned in our paper. Fortunately no action is required for them in the notebook!

[PCRandChill]

Thanks for the clarification, Kevin. Just to confirm, what I need to do is ensure that the antibody-antigen complex follows Chothia numbering and then plug it into the test_pdb variable in the prediction notebook? Also, is the DCCM map autogenerated, or do I need to generate it prior?

[athebault67]

Hello @kevinmicha, I am also interested in this answer regarding the generation of DCCM.
Moreover, when I try to run the Predicting affinity notebook by modifying the name of the PDB and changing the paths accordingly, and setting both renew_maps and renew_residues to True, I get this error:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/kevinmicha/Documents/all_structures/chothia/6fe4.pdb'
Are the paths hardcoded in the preprocessing.py file ?
Thanks in advance !