| # Benchmark structural inputs | |
| The protein and ligand structures of the benchmark. In total, there are 103 protein structures | |
| associated ligand binding poses that have been seperated in 14 sub-directories that indicate the were the input data was | |
| adapted from. | |
| ## Subset directories | |
| The names of each directory and the corresponding subset title in the [accompanying manuscript](https://doi.org/10.26434/chemrxiv-2022-p2vpg). | |
| * `bayer_macrocycles/`: Bayer Macrocycles | |
| * `charge_annhil/`: FEP+ charge change set | |
| * `fragments/`: FEP+ fragment data set | |
| * `gpcrs/`: GPCRs | |
| * `jacs_set/`: FEP+ R-group set | |
| * `janssen_bace/`: Janssen BACE1 data sets | |
| * `macrocycles/`: FEP+ macrocycles | |
| * `mcs_docking/`: MCS docking sets | |
| * `merck/`: The public Merck data set | |
| * `misc/`: Miscellaneous data sets | |
| * `opls_stress/`: OPLS stress set | |
| * `scaffold_hoping/`: FEP+ scaffold hopping | |
| * `waterset/`: FEP+ buried water set | |
| ### Subset directory contents | |
| Each directory contains | |
| * `subset_metadata.csv`. Metadata on each subsystem, the file naming scheme and the PDB each model was based on. | |
| * `*_ligands.sdf` The ligands along with additional rotomers and protomer/tautomer states. Each ligand is tagged with the | |
| experimental binding free energy (in kcal/mol). | |
| * `*_protien.pdb` The target structure. | |
| * `*_edges.csv` The edges of the perturbation graph along with experimental relative binding free energy. | |