This document describes how to find pockets in a Protein using the Deep Origin Pocket Finder.

Pockets¶

Creating Pockets¶

First, we create a Protein, for example, using:

from deeporigin.drug_discovery import  Protein, BRD_DATA_DIR
protein = Protein.from_file(BRD_DATA_DIR / "brd.pdb")
protein.remove_water()

Using Pocket Finder¶

Use the PocketFinder class from deeporigin.drug_discovery.pocket_finder to find pockets:

from deeporigin.drug_discovery import PocketFinder

pf = PocketFinder(protein, pocket_count=1)
pockets = pf.run()

pf.run() always runs the pocket finder (blocking) and returns a list of Pocket objects. Note that you will be charged for each run. To fetch previously computed pockets without re-running, use pf.get_results().

Estimating cost¶

To get a cost estimate without running the pocket finder, call quote() before run():

pf = PocketFinder(protein, pocket_count=1)
pf.quote()       # populates pf.estimate
pf.estimate      # estimated cost in dollars
pockets = pf.run()  # run when ready; pf.cost is set after completion

Using PDB Files¶

Create a pocket directly from a PDB file:

from deeporigin.drug_discovery import Pocket

pocket = Pocket.from_pdb_file("path/to/pocket.pdb", name="my_pocket")

From a residue number¶

Create a pocket centered on a specific residue:

from deeporigin.drug_discovery import Pocket

pocket = Pocket.from_residue_number(
    protein=protein,
    residue_number=123,
    chain_id="A",
    cutoff=5.0
)

From a Ligand¶

Create a pocket from a ligand structure:

from deeporigin.drug_discovery import Pocket, Ligand, BRD_DATA_DIR

ligand = Ligand.from_sdf(BRD_DATA_DIR / "brd-2.sdf")
pocket = Pocket.from_ligand(ligand, name="ligand_pocket")

From a result-explorer record ID¶

Load a single pocket by its result-explorer record ID (for example, an ID from a previous pocket-finder run or from the platform UI):

from deeporigin.drug_discovery import Pocket

pocket = Pocket.from_id("your-pocket-record-id")

This fetches the record, downloads the pocket PDB file, and returns a Pocket with properties populated from the record. Optionally pass a client if you do not want to use the default:

pocket = Pocket.from_id("your-pocket-record-id", client=my_client)

If no record exists for the given ID, ValueError is raised.

Visualization¶

Inspecting pocket data¶

View pocket properties by simply inspecting the object:

pocket

You should see a table similar to:

    Pocket:
    ╭─────────────────────────┬──────────────╮
    │ Name                    │ pocket_1     │
    ├─────────────────────────┼──────────────┤
    │ Color                   │ red          │
    ├─────────────────────────┼──────────────┤
    │ Volume                  │ 545.0 ų     │
    ├─────────────────────────┼──────────────┤
    │ Total SASA              │ 1560.474 Ų  │
    ├─────────────────────────┼──────────────┤
    │ Polar SASA              │ 762.11224 Ų │
    ├─────────────────────────┼──────────────┤
    │ Polar/Apolar SASA ratio │ 0.95459515   │
    ├─────────────────────────┼──────────────┤
    │ Hydrophobicity          │ 15.903226    │
    ├─────────────────────────┼──────────────┤
    │ Polarity                │ 17.0         │
    ├─────────────────────────┼──────────────┤
    │ Drugability score       │ 0.83243614   │
    ╰─────────────────────────┴──────────────╯

3D visualization in a Protein¶

Pockets can be visualized using:

protein.show(pockets=pockets)

You should see something like: