Surveying molecular interactions with DOT

  • Authors:

  • Lynn F. Ten Eyck;Jeffrey Mandell;Victoria A. Roberts;Michael E. Pique

  • Affiliations:

  • San Diego Supercomputer Center, Computational Center for Macromolecular Structure, P.O. Box 85608, San Diego, CA;San Diego Supercomputer Center, Computational Center for Macromolecular Structure, P.O. Box 85608, San Diego, CA;The Scripps Research Institute, Department of Molecular Biology, 10666 North Torrey Pines Road, La Jolla, CA;The Scripps Research Institute, Department of Molecular Biology, 10666 North Torrey Pines Road, La Jolla, CA

  • Venue:
  • Supercomputing '95 Proceedings of the 1995 ACM/IEEE conference on Supercomputing
  • Year:
  • 1995

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Abstract

The purpose of the molecular interaction program DOT (Daughter of Turnip) is rapid computation of the electrostatic potential energy between two proteins or other charged molecules. DOT exhaustively tests all six degrees of freedom, rotational and translational, and produces a grid of approximate interaction energies and orientations. It is able to do this because the problem is cast as the convolution of the potential field of the first molecule and any rotated charge distribution of the second. The algorithm lends itself to both parallelization and vectorization, permitting huge increases in computational speed over other methods for obtaining the same information. For example, a complete mapping of interactions between plastocyanin and cytochrome c was done in eight minutes using 256 nodes of an Intel Paragon. DOT is expected to be particularly useful as a rapid screen to find configurations for more detailed study using exact energy models.