Pocket Measure API

The Pocket Measure API runs the Rosetta pocket_measure protocol given an input PDB file and an option subset of residue. Pocket Measure API performs grid-based scoring around the protein to discover and measure pockets in cubic Angstroms. It will take a list of residue positions (RESIDUE:CHAIN) and determine the pocket size at each position.

By default, the API will run the protocol for all residues in the input pdb. You may specify a subset of residues to run the protocol on with the –residues flag. You can modify the minimum pocket size using the –min-size flag (default = 10 cubic Angstroms). If desired, set dump-pdb=”true” to get all pocket pdbs that contain the associated pocket grid for each residue. The job will output a score file for every residue provided or all residues in the input PDB, and optionally all pocket pdbs.

Command Line Interface

Examples

Run pocket measure on a particular residue with minimum pocket size of 12 cubic Angstroms

lev engine submit pocket-measure input.pdb \
    --residues 15:A 
    --min-size 12 
    --dump-pdb=true

Flags

  • --residues (str) (Default = all)
    • Comma separated list of residues to run pocket measure on (syntax should match RESIDUE:CHAIN)
  • --min-size (int332) (Optional)
    • Minimum pocket size to report (default = 10 cubic Angstroms)
  • --dump-pdb (bool) (Optional)
    • If true, output all pocket pdbs that contain the associated pocket grid for each residue (default = false)

Output

  • pocket_scores.csv
    • A per-residue csv file with the pocket size at each residue.
  • pdbs (Optional)
    • A directory of PDBs that contains the associated pocket grid for each residue.

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: