Additions:
- Added new baseline methods (AlphaFold 3, Chai-1 with multiple sequence alignments (MSAs))
- Added new binding site-focused implementation of
complex_alignment.pybased on PyMOL'saligncommand, which in many cases yields 3x better docking evaluation scores for baseline methods - Added new script for analyzing baseline methods' protein conformational changes w.r.t. input (e.g., AlphaFold) protein structures and the corresponding reference (crystal) protein structures
- Added the new centroid RMSD and PLIF-EMD/WM metrics (n.b., see new arXiv preprint for more details)
- Added a failure mode analysis notebook (n.b., see new arXiv preprint for more details)
Changes:
- Introducing DockGen-E, a new version of the DockGen benchmark dataset featuring enhanced biomolecular context for docking and co-folding predictions - namely, now all DockGen complexes represent the first (biologically relevant) bioassembly of the corresponding PDB structure
- For the single-ligand datasets (i.e., Astex Diverse, PoseBusters Benchmark, and DockGen), now providing each baseline method with primary and cofactor ligand SMILES strings for prediction, to enhance the biomolecular context of these methods' predicted structures - as a result, for these single-ligand datasets, now the predicted ligand most similar to the primary ligand (in terms of both Tanimoto and structural similarity) is selected for scoring (which adds an additional layer of challenges for baseline methods)
- Updated Chai-1's inference code to commit
44375d5d4ea44c0b5b7204519e63f40b063e4a7c, and ran it also with standardized (paired) MSAs - Replaced all AlphaFold 3 server predictions of each dataset's protein structures with predictions from AlphaFold 3's local inference code
Deprecations:
- Pocket-only benchmarking has been deprecated
Results:
- With all the above changed in place, simplified, re-ran, and re-analyzed all baseline methods for each benchmark dataset, and updated the baseline predictions and datasets (now containing standardized MSAs) hosted on Zenodo
- NOTE: The updated arXiv preprint should be publicly available by 02/12/2025
Full Changelog: v0.5.0...v0.6.0