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