Nanome - Docking

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

Supported Docking algorithms:

• Smina
• Autodock4

Dependencies

Docker

Usage

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

Development

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

License

MIT