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DRD3 docking (using TDC)

DRD3 docking (using TDC)#

Type of objective function: discrete Environment to run this objective function: poli tdc

About#

This objective function computes the docking score of a small molecule w.r.t. the protein 3pbl, which is the canonical example in the Therapeutics Data Common’s docking oracles [Huang et al., 2021]. Under the hood, it uses pyscreener, vina and the ADFR suite.

Prerequisites#

Installing AutoDock Vina#

Download the files#

Download AutoDock Vina from the Center for Computational Structural Biology’s website. Uncompress them.

Add the binary folder to the path.#

Add this to the path by including export PATH=path/to/AutoDock_vina/bin:$PATH in your ~/.bashrc or ~/.zshrc.

# In your ~/.bashrc or ~/.zshrc
export PATH=path/to/AutoDock_vina/bin:$PATH

Installing the ADFR suite#

Download the files#

Download the installable files. It’s likely that you will have to run the ./install.sh script inside the folder, and thus you might have to change its permissions for execution using chmod +x

Install it#

After running ./install.sh, you should be able to find .../bin/prepare_receptor.

Add prepare_receptor to the path#

For the docking to run, pyscreener needs access to the prepare_receptor binary. However, adding all of the ADFR bin folder is sometimes problematic, since it has a version of Python inside.

Thus, we recommend creating a symlink. Write this in your ~/.bashrc or ~/.zshrc:

# In your ~/.bashrc or ~/.zshrc
ln -sf /path/to/ADFR/bin/prepare_receptor /path/to/AutoDock_vina/bin

Making sure you’re all set#

If the set-up above was successful, you should be able to run

which vina
# /path/to/your/bin/vina

and

which prepare_receptor
# /path/to/your/bin/prepare_receptor

How to run#

import numpy as np
from poli.objective_repository import DRD3ProblemFactory, DRD3BlackBox

# Creating the black box
f = DRD3BlackBox()

# Creating a problem
problem = DRD3ProblemFactory().create()
f, x0 = problem.black_box, problem.x0

# Example input:
x = np.array(["c1ccccc1"])

# Querying:
y = f(x)
print(y)  # Should be close to -4.1
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