Recent advances in AutoDock: Search, representation and scoring


Garrett M. Morris1, Ruth Huey1, William Lindstrom1, Chenglong Li1, Yong Zhao1, William E. Hart2, Richard Belew3, Michel F. Sanner1, David S. Goodsell1, and Arthur J. Olson1. (1) Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., Mail Drop MB-5, La Jolla, CA 92037-1000, (2) Computational Sciences, Computer Sciences, and Mathematics Center, Sandia National Laboratories, PO Box 5800, MS 1110, Albuquerque, NM 87185, (3) Cognitive Computer Science Research Group, University of California, San Diego, Computer Science & Engr. Dept. (0114), La Jolla, CA 92093
Docking is often described as consisting of two major components: a scoring function and a search method. Implicit in this is the representation of the molecules being docked, and how new candidate dockings are generated. Recent developments in AutoDock in each of these areas will be presented, including the development of a new empirical free energy scoring function, new search and optimisation methods, and a novel representation of molecular flexibility able to incorporate motion of both domains and side-chains in proteins.

Thanks to on-going advances in computer hardware, AutoDock is able to benefit from a bold, new way to interact with computational chemistry code, by using an extensible, object-oriented interpreter.

Progress in ease-of-use of AutoDock, and applications in protein-protein docking, covalent docking, and in silico high-throughput screening (HTS), will also be presented.


Docking and Scoring
9:00 AM-12:20 PM, Monday, August 23, 2004 Pennsylvania Convention Center -- 109A, Oral

Division of Computers in Chemistry

The 228th ACS National Meeting, in Philadelphia, PA, August 22-26, 2004