Autodock
Background
AutoDock is a molecular modeling simulation software designed for protein-ligand docking, a technique to predict the position and orientation of a ligand (a small molecule) when it is bound to a protein receptor or enzyme.
AutoDock Vina is an improved version has an improved local search routine that makes use of multicore/multi-CPU computer setups. AutoDock Vina tends to be faster than AutoDock 4 by orders of magnitude.
In a recent study both software were tried on 800 protein–ligand complexes for which both PDB structures and experimental binding affinity are available. The title of the paper gives a brief summary “Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity” (Nguyen et al. J. Chem. Inf. Model. 2020, 60, 1, 204–211.)
Tutorials
This tutorial takes advantage of the Biochemitry cluster and to install and run both AutoDock and AutoDock Vina.
Since the cluster does not support graphical interface, all preparations and calculations are done in a text-driven manner.
TUTORIAL 1 Autodock Vina on Linux Cluster with HTCondor
(last updated: April 18, 2017 – recompiled April 2019)
- Autodock Vina on Linux Cluster with HTCondor: (same content, different formats)
- PDBQT exercise files: protein | ligand
REFERENCES:
- Stefano Forli, Ruth Huey, Michael E Pique, Michel F Sanner, David S Goodsell & Arthur J Olson (2016), “Computational protein–ligand docking and virtual drug screening with the AutoDock suite“ Nature Protocols 11: 905–919, doi:10.1038/nprot.2016.051
- Trott, O.; Olson, A.J. (2010), “AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading”, Journal of Computational Chemistry, 31 (2): 455–461, doi:10.1002/jcc.21334
External video tutorial(s)
AutoDock Vina Tutorial by Sari Sabban
The following 1h long tutorial provides a python script to prepare data without Autodock Tools and offers many useful tools.
The Python script used during the video can be downloaded from github: AutoDock.py
During the video ligands are pulled from the Zinc15 database:
- Zinc15: https://zinc15.docking.org
- Zinc15 Wiki: http://wiki.docking.org/index.php/Category:ZINC15