Published August 2, 2024 | Version v3

OpenFE Ligand Networks for the Protein Ligand Benchmark set

  • 1. Open Free Energy

Description

These are the OpenFE LigandNetworks for the 15 systems from the ProteinLigandBenchmark v0.3 (https://github.com/openforcefield/protein-ligand-benchmark)

- Kartograf mapper

- Lomap scorer

- OpenEye AM1BCC ELF10 partial charges

- MST networks

- allowing element changes

 

There are 10 systems that do not involve charge changing transformations, and 5 systems with transformations that involve a change in the net charge of the system (in folder `net_charge_changes`: cdk8, eg5, syk, thrombin, tnks2).

 

These .graphml files can be read into OpenFE using:

```

from openfe.setup import LigandNetwork

file = 'ligand_network.graphml'

with open(file) as f:

    graphml = f.read()

network = LigandNetwork.from_graphml(graphml)

```

Files

kartograf_mst_LigandNetworks.zip

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