Inputs for running the binding free energy benchmark

The inputs for the free energy benchmark are divided into two sections:

fep_plus_inputs/ which contains the inputs for the FEP+ software (e.g. fmp files) and the scripts required to run the benchmark.
structure_inputs/ which contain structural inputs in a format can be read by many computational chemistry platforms (i.e. PDB and sdf files).

This benchmark data set was constructed and validated using FEP+ and the data in the structure_inputs was derived from the FEP+ fmp graph files..

Arrangment of the input files

The benchmark data set consists of a number of congeneric series that have been grouped based on the publication where the inputs were based on. As documented in the supporting information of the accompanying manuscript, many systems were modified from their original source.

Metadata

Details on the congeneric series subset, file naming scheme, protein name, original PDB reference, experimental binding affinity dynamic range, number of input structures, and the DOI of the source on the source where the structures were taken from, can be found in the file below:

benchmark_metadata.csv

The Number of nodes column in benchmark_metadata.csv refers to the number of ligand structural inputs. Some ligands had multiple structural inputs as they were represented by multiple rotamers or protomer/tautomers.