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Add FreeSolv #104

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6ef6b4e
add first pass at freesolv
jthorton Feb 12, 2026
2b9c5ab
add other charge types, fix test index, update failed molecules list
jthorton Feb 13, 2026
efd0c4e
Merge branch 'refs/heads/main' into freesolv
jthorton Feb 16, 2026
35571bb
update reference data format, fix tests
jthorton Feb 16, 2026
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5 changes: 4 additions & 1 deletion openfe_benchmarks/data/benchmark_system_indexing.yml
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Expand Up @@ -67,11 +67,14 @@ water_set:
taf12: ["protein", "bfe"]
thrombin: ["protein", "bfe"]
urokinase: ["protein", "bfe"]
solvation_set:
freesolv: ["sfe"]
metadata:
last_updated: "2026-02-13"
last_updated: "2026-02-16"
notes:
- "Systems may or may not include cofactor files"
- "All systems can be used for ASFEs and RSFEs"
- "sfe tags indicate that a system has experimental salvation free energy data available"
- "bfe tag indicates that experimental binding free energy data is available for this system"
- "Systems with proteins can also be used for RBFE and ABFE calculations"
- "Systems with ligands and cofactors could potentially be used for RBFE and ABFE calculations"
17 changes: 17 additions & 0 deletions ...benchmarks/data/benchmark_systems/solvation_set/freesolv/PREPARATION_DETAILS.md
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@@ -0,0 +1,17 @@
Done by Joshua Horton on 2026-02-12

All ligands extracted from the FreeSolv database version https://github.com/MobleyLab/FreeSolv/releases/tag/v0.52



## Notes

The reference data was generated using the [generate_freesolv_exp_data.py](../../../data_generation/generate_freesolv_exp_data.py) script using the [conda-lock_linux-64.yml](../../../data_generation/conda-lock_linux-64.yml) environment.
Charges were generated using the [charge_freesolv.py](../../../data_generation/charge_freesolv.py) script using the [conda-lock_linux-64.yml](../../../data_generation/conda-lock_linux-64.yml) environment.
Some ligands could not be charged with all methods, the following lists the ligands that could not be charged with each method:
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@hannahbaumann hannahbaumann Feb 16, 2026

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Would we want to add a ligand network for these, or not for now?

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@jthorton jthorton Feb 16, 2026

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I'll say no for now, as I don't think this will be needed yet and don't want to confuse people. We can add when needed?


- am1bccelf10_oe:
- mobley_7176248

- am1bcc_at:
- mobley_9741965
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