Once you have installed the package, you will have access (among others)
This module offers a simple API to define and visualize
nglview) subpockets and regions within a pocket.
from opencadd.structure.pocket import Pocket pocket = Pocket.from_file( filepath="protein.mol2", # Dummy file path pocket_residue_pdb_ids=[50, 51, ..., 198], name="example kinase", pocket_residue_labels=[1, 2, ..., 85] )
Currently, the main focus of this module is the definition of subpockets within a pocket.
As an example, we add here a kinase subpocket called
"hinge", which will be
visualized in magenta and whose center is calculated based on the CA atoms of residues 73, 128, and
193 (residue PDB IDs). These residue PDB IDs correspond to the KLIFS alignment IDs 16, 47, and 80.
pocket.add_subpocket( name="hinge", anchor_residue_pdb_ids=[73, 128, 193], color="magenta", anchor_residue_labels=[16, 47, 80] # Optionally )
Usually, it is helpful to highlight the pocket region, which inspired the subpocket choice, hence the module allows definitions of important pocket regions.
In our example, the subpocket
"hinge" is intended to target one of the most important
regions in kinases, the hinge region, where kinase inhibitors form hydrogen bonds with the kinase.
We use the hinge region residues to add a region to our
pocket.add_region( name="hinge region", residue_pdb_ids=[127, 128, 129], color="magenta", residue_labels=[46, 47, 48] # Optionally )
Visualize the pocket
Now we can visualize the pocket using:
Check out our tutorial to find out more!