AutoDock

Author

Garrett M. Morris, David S. Goodsell, Ruth Huey, William E. Hart, Scott Halliday, Rik Belew and Arthur J. Olson

Origin

The Scripps Research Institute

Version

AutoDock 4.0.1

Official Web Site

http://autodock.scripps.edu/

Brief Program Description

AutoDock is a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

Areas of Application

AutoDock has applications in:

• X-ray crystallography

• Structure-based drug design

• Lead optimization

• Virtual screening (HTS)

• Combinatorial library design

• Protein-protein docking

• Chemical mechanism studies

New features in AutoDock 4.0.1 include:

• More accurate and reliable docking results

• An option to model flexibility in the target macromolecule

• An option to model flexibility in the target macromolecule

AutoDock 4.0.1 consists of two main programs: autodock4 performs the docking of the ligand to a set of grids describing the target protein; autogrid4 pre-calculates these grids.

For more information about the new functionality in AutoDock 4, users are referred to the following link on the AutoDock website: http://autodock.scripps.edu/wiki/NewFeatures

Implementation and Access

AutoDock can be accessed on Magellan by the command runautodock as follows:

$CHEM/runautodock progname [options]

where progname can be autodock4 or autogrid4

The software runs in serial only.

Machines

Available on Magellan.

Documentation

A Unix-style man page is available online, gives a summary of the implementation and the options available for the software, accessible by typing: man runautodock.

There is no specific User Guide for AutoDock 4.0.1. Users are referred to the AutoDock 3.0 User Guide which is available in PDF format from the directory $CHEM/doc/autodock3.0. A set of example files can be found in the directory $CHEM/autodock-4.0.1/examples

Literature References

References on the methods developed and used in the package are available in the AutoDock User Guide.

Specialist Support

Dr Helen Tsui. Address: Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ. Tel: 020 7594 1220 Email: helen.tsui@imperial.ac.uk.

Program Restrictions and Comments

There is a graphical user interface called AutoDockTools which is currently not available on Magellan but can be downloaded by the user from:

http://autodock.scripps.edu/resources/adt/index_html