scipion-chem-autodock

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Over the years, it has been modified and improved to add new functionalities, and multiple engines have been developed.

Installation

A) Requirements

In order to use this plugin, you need to install first scipion-chem.

B) Installation steps

• Install the stable version

  Through the plugin manager GUI by launching Scipion and following Others >> Plugin Manager, or

scipion3 installp -p scipion-chem-autodock

• Developer’s version

  1. Download repository:

  git clone https://github.com/scipion-chem/scipion-chem-autodock.git

  2. Install:

  scipion3 installp -p /path/to/scipion-chem-autodock --devel

Warning

Installation of the stable version through the Plugin Manager or with the command provided above is not available yet.

Please install the developer version until a stable version is released, or install the latest stable version with the following steps:

cd /path/to/scipion-chem-autodock && git checkout master && scipion3 installp -p . --devel

C) Packages & enviroments

Packages installed by this plugin can be located in /path/to/scipion/software/em/.

The following packages will be created:

TODO: COMPLETE THIS PART

Where version is the current version of that specific package.

Warning

These environments are used by the code in the different plugins, and we strongly advise not to modify them manually in order to keep their functions.

Protocols

A) Receptor preparation

• Receptor preparation: Prepares an AtomStruct object containing a protein file to make it ready for AutoDock tools, such as docking with AutoDock or Vina.

B) Ligand preparation

• Ligand preparation (prepare_ligand4.py): Uses the script prepare_ligand4.py in the utilities of AutoDock Tools to prepare a SetOfSmallMolecules.

• Ligand preparation Meeko: Uses the new Meeko functionality as a Python module to prepare a SetOfSmallMolecules.

C) Grid generation

• Grid generation: Generates the grids used by the different AutoDock programs using autogrid4.

D) Binding site identification

• AutoLigand Binding Site prediction: Uses AutoLigand tool to predict the binding sites on a protein receptor.

• AutoSite Binding Site prediction: Uses AutoSite tool to predict the binding sites on a protein receptor.

E) Pharmacophore generation

• AutoSite Pharmacophore Generation: Generates a Pharmacophore object RDKit compatible from a resulting binding site of AutoSite.

F) Docking

• AutoDock4 Docking: Uses AutoDock4: tool to predict the binding poses for a set of small molecules over the receptor.

• AutoDock-GPU Docking: Uses AutoDock-GPU:, the GPU implementation of AutoDock.

• Vina Docking: Uses AutoDock Vina: docking engine to predict the binding poses for a set of small molecules over the receptor.

G) Docking Rescoring

• AutoDock4 Dock Rescoring: Scores a SetOfSmallMolecules that has been already docked by any docking program using AutoDock4: scoring function.