Folding Stability Benchmark¶
Purpose¶
This benchmark evaluates the ability of a machine-learned interatomic potential (MLIP) to maintain the structural integrity of experimentally determined protein conformations during molecular dynamics (MD) simulations.
Description¶
Starting from an experimentally derived X-ray or NMR structure, the benchmark performs an MD simulation using the MLIP model in the NVT ensemble at 300 K for 250,000 steps (250 ps), leveraging the jax-md, as integrated via the mlip library, starting from a solvated structure.
Performance is quantified using the following metrics:
Retention of the original protein fold, via RMSD and TM-score.
Retention of secondary structure elements, via Secondary Structure matching (using DSSP).
Overall compactness, via Compactness (radius of gyration analysis).
For more information on each metric, please refer to the following pages:
Dataset¶
The dataset is composed by a series of protein structures taken from the PDB databank. They have the following IDs:
