DOT 2.0: Macromolecular Docking Software

	DOT 2.0 is available for download. Please sign up for the dot-announce mailing list for further notifications To contact the dot team please email dot-help@sdsc.edu.

• Introducing DOT 2.0
• Mailing Lists
• Documentation
• Download
• Publications
• Acknowledgements

Introducing DOT 2.0

Please acknowledge your use of DOT by citing:

• Roberts, Victoria A. and Thompson, Elaine E. and Pique, Michael E. and Perez, Martin S. and Ten Eyck, L. F., (2013) "DOT2: Macromolecular docking with improved biophysical models" Journal of Computational Chemistry, Volume 34, Issue 20, pages 1743-1758, 30 July 2013
  DOI: 10.1002/jcc.23304

DOT is a software package for docking macromolecules, including proteins, DNA, and RNA. DOT performs a systematic, rigid-body search of one molecule translated and rotated about a second molecule. The intermolecular energies for all configurations generated by this search are calculated as the sum of electrostatic and van der Waals energies. These energy terms are evaluated as correlation functions, which are computed efficiently with Fast Fourier Transforms. In a typical run, energies for about 108 billion configurations of two molecules can be calculated in a few hours on a few desktop workstations working in parallel.

The significantly enhanced new version of the DOT software package provides the following:

• Automated setup of DOT input files starting with protein coordinate files from the PDB.
• Improvements in molecular potentials that have been described in literature are now part of the automated setup.
• Error checking during setup of input files to detect potential problems before the docking calculation is run.
• Faster - DOT now runs 33% faster.
• Portability - will run on Linux, Mac OS X, and Solaris.
• Reevaluation of top-ranked DOT protein-protein complexes with ACE (pairwise atomic contact energy), which takes into account desolvation energy.

DOT has been successfully applied to stable protein-protein interactions, to the transient interactions between electron-transfer proteins, and to protein-DNA interactions. DOT's rigid-body docking has done well in the CAPRI (Critical Assessment of PRediction of Interactions http://capri.ebi.ac.uk/) experiments, in which predictions, usually based on unbound protein structures, are submitted before the structure of the complex is available.

The combination of computational docking results from DOT with experimental data has proved to be a powerful tool for understanding molecular interactions. Docking results can help to interpret biochemical data by putting it into a structural context, can guide the design of new experiments to further explore macromolecular interactions, and can, by providing a large set of candidates, reveal complexes that best fit biochemical or spectroscopic data.

Documentation

Please consult the following DOT documentation:
www.sdsc.edu/CCMS/DOT

• DOT 2.0 License
• DOT 2.0 User's Guide (PDF) Last update: May 30, 2013, (now searchable)
• FAQ

Mailing Lists

The CCMS team supports two DOT related mailing lists:

• dot-announce: A low-traffic list for announcements regarding bugs and new versions of the software
  dot-announce web page
  dot-announce archives
• dot-users: A forum for discussion of DOT, troubleshooting, and reporting potential bugs
  dot-users web page
  dot-users archives

Download DOT

Please complete this registration form to download DOT 2.0. You will receive a link to a page containing documentation and precompiled binaries for several popular platforms.

The CCMS folks really, really hate spam and really, really respect your privacy. We use your provided information only to send you the link to the download and to compile statistics for our grant sponsors.

We provide binaries for the following platforms and architectures:

• Mac OS X (Intel or Power PC)
• Solaris 8 (Sun SPARC)
• Red Hat Linux (Intel)

Publications

Acknowledgements

NIH GM-070996
NSF DBI 9616114
NSF DBI 9616115