v.0.5.0

What's Changed

Additions:

• Adds results with AlphaFold 3 predicted structures (now the default), which yield a 5-10% performance improvement over ESMFold structures on average
• Adds results for the new Chai-1 model from Chai Discovery
• Adds a new inference sweep pipeline for HPC clusters to allow users to quickly run an exhaustive sweep of all baseline methods, datasets, and tasks e.g., using generated batch scripts and a SLURM scheduler

Updates:

• Updates all Zenodo links to point to the latest version of the project's Zenodo record, which now includes the above-mentioned AlphaFold 3 predicted structures and baseline method results using them
• Updates documentation project-wide according to the additions listed above

Fixes:

• Fixes some CI testing issues

New Contributors

• @amorehead made their first contribution in #7

Full Changelog: v0.4.0...v0.5.0

v0.4.0

Full Changelog: v.0.3.0...v0.4.0

Updates:

• Renamed src root directory to posebench to support pip packaging
• Updated dataset documentation in README.md

Additions:

• Added and documented pip installation option
• Added mmCIF to PDB file conversion script
• Added apo-to-holo predicted protein structure accuracy assessment and plotting script
• Added support to notebooks/dockgen_inference_results_plotting.ipynb for analyzing the protein-ligand interactions within the PDBBind 2020 dataset's experimental structures

v0.3.0

v0.3.0 Release Notes

Additions:

• Added a notebook for plotting expanded DockGen benchmark results
• Added support for scoring relaxed-protein predictions

Corrections:

• Fixed runtime error for relaxed-protein energy minimization
• Fixed runtime error for compute benchmarking RoseTTAFold-All-Atom predictions

v0.2.0

v0.2.0 Release Notes

Additions:

• Added P2Rank as a new binding site prediction method available to use with AutoDock-Vina
• Added OpenJDK to the PoseBench Conda environment to enable P2Rank inference
• Added a script to benchmark the required compute resources for each baseline method

Updates:

• Updated citation

Corrections:

• Corrected directory navigation instructions (i.e., cd references) in README.md to reflect the directory structure of each Zenodo archive file
• Corrected Biopython, NumPy, and ProDy versions in the DiffDock Conda environment to avoid GCC compilation errors

v0.1.0

Initial public release with Sphinx documentation deployment.