Docking¶

This document describes how to dock a set of ligands to a protein using Deep Origin tools.

Prerequisites¶

We assume that we have an initialized and configured Complex object:

from deeporigin.drug_discovery import Complex
sim = Complex.from_dir("/path/to/folder/")
sim.connect()

For more details on how to get started, see Getting Started .

Starting a docking run¶

To dock all ligands to the protein, parallelizing and batching across all ligands, we do the following:

sim.docking.run(
    box_size=(15, 15, 15),      # match to your protein
    pocket_center=(13, -6, 22), # match to your protein
)

Controlling batch size

By default, all ligands are docked in batches of 32 ligands.

This can be controlled in two ways. First, you can control the batch size using the batch_size parameter.

sim.dock(
    batch_size=32,
    box_size=(15, 15, 15),      # note: tuple  
    pocket_center=(13, -6, 22), # note: tuple  
)

You can also specify the number of workers using:

sim.dock(
    n_workers=2,
    box_size=(15, 15, 15),      # note: tuple  
    pocket_center=(13, -6, 22), # note: tuple  
)

You can specify either the number of workers or the batch size, but not both.

This queues up tasks on Deep Origin. When it completes, the results of docking can be viewed.

Viewing status of docking¶

The status of docking runs can be viewed using:

sim.get_status_for("Docking")

Expected output

A typical output can look like:

{'ccdb9ba9-b3d2-4083-bb4c-7c7249f7dbc2': 'Succeeded',
 '17a0b478-c11d-48a9-9bce-2e0272b804fb': 'Running',
 '08342c26-b773-4423-91c3-3fcbe4955778': 'Running'}

The keys are IDs of the jobs running on Deep Origin. You may see different numbers of jobs based on your batch_size parameter and the number of ligands in your dataset.

Results¶

Viewing results¶

After completion of docking, we can view results using:

sim.docking.show_results()

This shows a table similar to:

Docking results

Viewing docked poses¶

To view the docked poses of all ligands in the complex, use:

sim.docking.show_poses()

Exporting for further analysis¶

To obtain the raw dataframe for further analysis, use:

df = sim.docking.get_results()

Exporting a SDF with docked poses¶

To export a SDF with docked poses, use:

sim.docking.get_poses("/path/to/output.sdf")

This generates a SDF file with the docked poses for all ligands in the Complex.