Pocket Relax API

The Pocket Relax API runs the Rosetta pocket_relax protocol given an input PDB file and an option subset of residue. Pocket Relax API performs Rosetta Relax conformational sampling around the protein, both with and without pocket formation biasing using a weighted pocket score term.

The pocket-relax API will take a list of residue positions (RESIDUE:CHAIN) and run the Rosetta Pocket Relax protocol. By default, the API will generate relax ensembles of 10 structures for each residue, for each pocket weight (0.15, 0.25, and 0.5) and also run an additional minimization step for each output structure in comparision to the input structure (no pocket weights). We provide these scores to allow users to select the best pocket weights for their pocket of interest. We suggest selecting pockets and weights that are within reasonable energy ranges compared to input reference results.

Once an optimal weight and pocket are selected, you can then scale up the sampling and run with –weight, –repeats, –pocket-only=true to generate your full scale relax ensemble.

Command Line Interface

Examples

Run pocket relax 100 times on a particular residue.

lev engine submit pocket-relax input.pdb \
    --residues 15:A \
    --repeats 100 \
    --pocket-only=true

Flags

  • --residues (str) (Default = all)
    • Comma separated list of residues to run pocket relax on (syntax should match RESIDUE:CHAIN)
  • --weight float (list) (Default = [0.15, 0.25, 0.5])
    • Pocket weight(s) to use for relax ensembles.
  • --pocket-only (bool) (Default = false)
    • Only generate relax ensembles for the specified pocket.
  • --repeats (int) (Default = 10)
    • Number of relax ensembles to generate for each pocket weight.

Output

  • pocket_relax_scores.csv
    • A csv file with the Rosetta scores for each relax model at each pocket weight.
  • pdbs (Optional)
    • A directory of PDBs that contains the relax models.

References

David K Johnson, John Karanicolas. Druggable Protein Interaction Sites Are More Predisposed to Surface Pocket Formation than the Rest of the Protein Surface. https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002951

Updated: