This application in Rosetta3 was created and documented by David Johnson, et al.
This application takes in a PDB file and specified target residue/residue pair and, generates a (localized) PocketGrid, identifies the exemplar, and outputs it to a file. See the 2013 paper for PocketGrid algorithm details and the 2015 for exemplar creation algorithm details.
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
Sample command
make_exemplar.linuxgccrelease -database ~/Rosetta/main/database -in:file:s input.pdb -central_relax_pdb_num 97:A,143:A -pocket_grid_size 12 -pocket_static_grid -pocket_filter_by_exemplarmake_exemplar options
General Rosetta Options
-database Path to rosetta databases
-in:file:s Input pdb file(s)
Pocket Identification Options
-pocket_num_angles Number of different pose angles to measure pocket score at, default is 1, but at least 100 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_probe_radius Radius of surface probe molecule, default 1.0 Angstroms
-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_limit_exemplar_color During clustering of exemplar atoms into exemplars, do not allow exposed color elements that are farther than 3 Angstroms apart to cluster together, creating a more concise exemplar, default=true
-pocket_limit_small_exemplars Ignore exemplars with fewer than 5 hydrophobic atoms, default=true
-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