PoseBusters Benchmark (PoseBusters Benchmark Set)

These are the protein-ligand complexes of the PoseBusters Benchmark set as described in the paper "PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences" [1] with associated code at https://github.com/maabuu/posebusters

All protein-ligand complexes were originally submitted to the Protein Data Bank (PDB) [2]. The PoseBusters Benchmark set was curated by us using the PDB and contains 308 cases. All complexes were downloaded from the PDB as MMTF [4] files and processed with PyMOL [5].

Note: During peer review we learned that some of the 428 structures contain crystal contacts (e.g. 5S8I_2LY). For the journal paper the results are reported on a subset containing 308 structures. The IDs for this subset can be downloaded here: https://github.com/maabuu/posebusters/files/14516485/posebusters_pdb_ccd_ids.txt

References

[1] Buttenschoen M, Morris GM, Deane CM. PoseBusters: AI-based docking methods fail to generate physically valid poses or generalise to novel sequences. arXiv; 2023. Available from: http://arxiv.org/abs/2308.05777

[2] H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne, The Protein Data Bank (2000) Nucleic Acids Research 28: 235-242 https://doi.org/10.1093/nar/28.1.235.