Vinalooper

virtual screening script for AutoDock Vina

Download // How To Install // Usage // Tutorial // FAQ // Contact

Vinalooper

Vinalooper is a python script that automates the docking of compounds against a protein using AutoDock Vina. The Open Babel chemical toolbox is employed for extracting compound PDB files from a single library SDF file. AutoDockTools is used for preparing the compound and protein PDBQT files, and Vina is used for docking.

How to install

Under Debian
sudo apt-get install autodocktools
sudo apt-get install autodock-vina
sudo apt-get install openbabel
sudo apt-get install python-openbabel

Download Vinalooper, move to /usr/local/bin


Linux
Download and Install AutoDockTools
Download and Install AutoDock Vina
Download and Install Open Babel
Download and Install Open Babel Python Modules

Download Vinalooper and move to /usr/local/bin


Mac OSX (untested)
Download and Install AutoDockTools
Download and Install AutoDock Vina
Download and Install Open Babel
Download and Install Open Babel Python Modules

Download Vinalooper


Windows
in development

Usage

python vinalooper.py arguments
	-i	input SDF file
	-r 	receptor PDB file
	-x	x dimension (angstroms)
	-y	y dimension (angstroms)
	-z	z dimension (angstroms)
	-xc	x offset (angstroms)
	-yc	y offset (angstroms)
	-zc	z offset (angstroms)
	-o	output directory
	-n	"any notes to save"
Eg: python vinalooper.py -i ligands.sdf -r receptor.pdb -x 20 -y 20 -z 20 -xc 4.5 -yc -5.6 -zc 14.2 -o myoutput -n "some notes"
Alternatively no arguments passed runs vinalooper in interactive mode: python vinalooper.py

Tutorial

Frequently Asked Questions

What settings are used for preparing ligands and proteins?
Ligands are prepared with prepare_ligand4.py (AutoDockTools) with no arguments. Receptor proteins are prepared with prepare_receptor4.py (AutoDockTools) with no arguments.

What exhaustiveness level is Vina ran at?
The default: 8.

What should the grid size be limited to?
About 20x20x20. Note: Vina uses 1 angstrom as units, AutoDock uses 0.375 angstrom, so if you use AutoDock to obtain grid coordinates than adjust spacing to 1 angstrom. Alternative to AutoDock, use PyMOL with Autodock/Vina plugin to obtain grid coordinates.

Contact

email: stefanhinote[at]email.arizona.edu