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- Title
LGA-Dock/EM-Dock — Exploring Lamarckian genetic algorithms and energy-based local search for ligand–receptor docking.
- Authors
Wiley, E. Ashley; MacDonald, Michael; Lambropoulos, Andreas; Harriman, D. Joseph; Deslongchamps, Ghislain
- Abstract
We report the development of LGA-Dock and EM-Dock, two SVL-based docking programs for flexible ligand – rigid receptor docking applications. LGA-Dock is comprised of a stochastic population generator, a docking routine based on a Lamarckian genetic algorithm, and a local search function based on molecular mechanics (MM) energy minimization. Subsequent modifications of LGA-Dock to address performance issues produced EM-Dock, which proved to be as accurate and much faster than its predecessor despite the deletion of the genetic algorithm component. The basic performance of LGA-Dock and EM-Dock, compared with AutoDock and MOE™ 2004.03 docking routines is presented.
- Subjects
GENETIC algorithms; SIMULATED annealing; QUANTUM theory; RECEPTOR-ligand complexes; COMBINATORIAL optimization
- Publication
Canadian Journal of Chemistry, 2006, Vol 84, Issue 3, p384
- ISSN
0008-4042
- Publication type
Article
- DOI
10.1139/V06-012