piercelab/antibody_benchmark

Antibody-Antigen Docking and Affinity Benchmark

antibody_benchmark's Issues

Potential Mismatches between bound and unbound pdbs

I'm getting very large RMSD's between unbound/bound receptor chains for a few targets.

Upon further inspection, it almost appears that the bound and unbound chains have

I'm not sure, but e.g. 6B0S is listed as an easy target, yet the receptor bound/unbound RMSD is >10A.

This is not the only target exhibiting this issue, some others are 5CX7 and 3JM9 (plus a few more). Is this normal?

Questions about antibody structure data format

Hi! I have a few questions regarding the antibody structures in the dataset:

1. As far as I understand, the bound structures are obtained from SAbDab, then the corresponding unbound structures are searched from the PDB. Are the antibody structures in either the bound or unbound conformations already renumbered by one of the numbering systems (e.g. SAbDab has Chothia numbered structures)?
2. In the summary file antibody_antigen_cases.txt, for the "Complex PDB" columns, when there are two antibody chains, are these consistently listed as heavy chain id followed by light chain id?

Thank you for curating such a valuable dataset!