DOT 2.0 - Macromolecular Docking Software Search CCMS Software CCMS Info DOT 2.0: Macromolecular Docking Software DOT 2.0 is for download. Please for the dot-announce mailing list for further notifications To contact the dot team please. • • • • • • 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) ' 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. Emphasis Art Ninth Edition Sharon. 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. Dist Update Opensuse. • 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 (Critical Assessment of PRediction of Interactions ) 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.