Nanome - Docking

A Nanome Plugin to interface with a variety of docking softwares to dock ligands to a receptor.

Supported Docking algorithms:

Dependencies

The docking algorithm used is determined by the --algorithm flag on startup. It flag not provided, it defaults to smina

To run Smina Docking in a Docker container:

$ cd docker
$ ./build.sh
$ ./deploy.sh [args]

To run Docking with Autodock4:

$ cd docker
$ ./build.sh --build-arg ALGORITHM=autodock4
$ ./deploy.sh --algorithm autodock4 [args]

In Nanome:

Activate Plugin, Docking window will automatically open
Select a receptor
Click on “Ligand”, and select ligands to dock
If using Smina, click on “Site”, and select which molecule should be used to define the docking site
Choose number of poses to return for each ligand
Choose size of the box to generate around the site molecule (Smina only)
Click Run

To run Docking with autoreload:

$ python3 -m pip install -r requirements.txt
$ python3 run.py <algorithm> -r [args]

algorithm can be (smina | autodock4)

Note for autodock4: The adfr-suite conda environment must be set up to run code requiring Python 2.7

$ conda env create --file adfr-suite.yml

MIT