fep_benchmark_inputs/structure_inputs/README.md

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.

• 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.