DOT 2.0: Macromolecular Docking Software
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:
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.
Please consult the following DOT documentation:
The CCMS team supports two DOT related mailing lists:
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.
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We provide binaries for the following platforms and architectures:
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.
|Last revision: May 7, 2013||San Diego Supercomputer Center|
|URL: http://www.sdsc.edu/CCMS/DOT/||© Copyright 2007 University of California at San Diego|