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

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:

• DOT 2.0 License
• DOT 2.0 User's Guide (PDF) Last update: April 1, 2008, Reformatted October 1, 2008 (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

Key papers on DOT

Mandell, J. G., Roberts, V. A., Pique, M. E., Kotlovyi, V., Mitchell, J. C., Nelson, E., Tsigelny, I., and Ten Eyck, L. F., (2001) "Protein Docking Using Continuum Electrostatics and Geometric Fit", Prot. Eng., 14, 105-113.

Ten Eyck, L. F., Mandell, J., Roberts, V. A., and Pique, M. E., (1995) "Surveying Molecular Interactions With DOT", in Proceedings of the 1995 ACM/IEEE Supercomputing Conference, San Diego, IEEE Computer Society Press, Los Alamitos, California.

Application of DOT to protein-DNA interactions

Fan, L. and Roberts, V. A., (2006) "Complex of linker Histone H5 with the Nucleosome and Its Implications for Chromatin Packing", Proc. Nat. Acad. Sci. U.S.A., 103, 8384-8389.

Roberts, V. A., Case, D. A., and Tsui, V., (2004) "Predicting Interactions of Winged-Helix Transcription Factors with DNA", Proteins, 57, 172-187.

Adesokan, A. A., Roberts, V. A., Lee, K. W., Lins, R. D., and Briggs, J. M., (2003) "Prediction of HIV-1 Integrase/Viral DNA Interactions in the Catalytic Domain by Fast Molecular Docking" J. Med. Chem., 47, 821-828.

Application of DOT to protein-protein interactions

Roberts, V. A. and Pique, M. E., (1999) "Definition of the Interaction Domain for Cytochrome c on Cytochrome c Oxidase: III. Prediction of the Docked Complex by a Complete, Systematic Search", J. Biol. Chem., 274, 38051-38060.

Additional methods/evaluation papers

Law, D. S., Ten Eyck, L. F., Katzenelson, O., Tsigelny, I., Roberts, V. A., Pique, M. E., and Mitchell, J. C., (2003) "Finding Needles in Haystacks: Reranking DOT Results by Using Shape Complementarity, Cluster Analysis and Biological Information", Proteins, 52, 33-40.

Acknowledgements

NIH GM-070996
NSF DBI 9616114
NSF DBI 9616115