This application in Rosetta3 was created and documented by David Johnson, et al.

# Purpose and Algorithm

This application is intended to automate the pocket optimization process, which previously had been done in two parts. Relax is performed and then the Pocket constraint is turned off an a full atom minimization is performed. If the pocket constraint is not used, it performs a simple relax and minimization, which is used to generate the unconstrained decoy comparison set.

# References

Johnson DK and Karanicolas J. Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface. PLoS Comput Biol. 2013;9(3):e1002951 Johnson DK and Karanicolas J. Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations. PLoS Comput Biol. 2015;11(2):e1004081

# Command Line Options

Sample command

pocket_relax.linuxgccrelease -database ~/Rosetta/main/database -in:file:s input.pdb -pocket_max_size 300 -pocket_num_angles 2 -score:patch pocket.wts.patch -cst_fa_file constraints -nstruct 1000 -pocket_zero_derivatives

make-exemplar options

General Rosetta Options
-database                   Path to rosetta databases
-in:file:s                  Input pdb file(s)
See [[Relax  | application_documentation/relax]] documentation for other options

Pocket Constraint Options
-score:patch                The PocketConstraint needs to be turned on
-cst_fa_file                The PocketConstraint target residue and weight is specified here
-pocket_zero_derivatives    The PocketConstraint has no derivitive, and this flag specifies to return derivitives of 0 during minimization phases of Relax

Pocket Identification Options
-pocket_num_angles          Number of different pose angles to measure pocket score at, default is 1, but 2 is recommended to reduce grid and orientation artifacts
-pocket_grid_size           Defines the dimensions of the PocketGrid centered on the target residue(s), or 10 Angstroms by default
-pocket_psp                 Mark Pocket-Solvent-Pocket events as well, default=false
-pocket_sps                 Unmark Solvent-Pocket-Solvent events, default=true
-pocket_surface_dist        Distance to consider pocket point being "surface" and excluded from "deep volume"
-pocket_max_spacing         Maximum residue-residue distance to be considered a pocket, default is 12 Angstroms
-pocket_min_size            Minimum pocket size to score, in cubic Angstroms, default is 10 cubic Angstroms
-pocket_max_size            Maximum pocket size to report, in cubic Angstroms, 0 for no limit (default)
-pocket_side                Include only side chain residues for target surface, default=false
-pocket_filter_by_exemplar  Additional filter generates an exemplar and then restricts the pocket to that exemplars, defaul=false
-pocket_ignore_buried       Ignore pockets that are not solvent exposed, default=true
-pocket_only_buried         Identify only pockets buried in the protein core (automatically sets -pocket_ignored_buried false), default=false
-pocket_static_grid         By default the PocketGrid expands if pocket points are identified near the edge, this flag disables the autoexpanding feature.
-pocket_grid_spacing        Defines the spacing of the PocketGrid, 0.5 by default

pocket.wts.patch file

pocket_constraint = 1.0

constraints file format

Pocket 0.25 97:A,143:A

# Tips

• Orientation artifiacts can have an artificial impact on pocket volume, therefore specifying -pocket_num_angles of 2 is suggested to reduce that effect
• -pocket_max_size is not necessary, however it can be useful when a given protein is able to open massive pockets that are not relevant for inhibition. -pocket_max_size essentially caps the volume returned by the PocketConstraint, at which point a pocket will grow ONLY when it is energetically favorable to do so.