Validation data#

The MD trajectories used to validate PHENOMS on real systems (EGFR WT vs. del747-749, and PLCg2) are hosted on Zenodo rather than in this repository — too large for git, and a stable, citable DOI is the point.

DOI: 10.5281/zenodo.22879722 (CC0 1.0 license)

Contents#

  • EGFR — wild-type and del747-749 deletion mutant, 3 replicates each. CHARMM force field, GROMACS engine. Protein-centered/fitted multi-frame PDB trajectories.

  • PLCg2 — wild-type. AMBER force field, AMBER engine. Topology (.prmtop) plus a 3500 ns trajectory (.nc).

Getting the data#

python scripts/fetch_zenodo_data.py             # both datasets (~8.5GB)
python scripts/fetch_zenodo_data.py --egfr-only  # ~1GB
python scripts/fetch_zenodo_data.py --plcg2-only # ~7.5GB

This downloads into protein_pdb_exports/ (EGFR) and plcg2_data/ (PLCg2) at the repository root — the same paths the benchmark scripts already expect (see scripts/renumber_pdb_to_reference.py and docker/README.md’s PLCg2 section).

Using it#

EGFR WT and the del747-749 mutant are numbered differently, so align them first:

python scripts/renumber_pdb_to_reference.py \\
    --reference protein_pdb_exports/3_19_26_wt_rep_1_protein_centered_fit_nopbc.pdb \\
    --mobile protein_pdb_exports/3_19_26_del747-749_rep1_protein_centered_fit_nopbc.pdb

Then load both sets with SimulationSet / ComparisonSet as usual (see Usage).

For PLCg2, see the “PLCg2 truncation benchmark” section of docker/README.md.