Assessing search strategies for flexible docking

  title={Assessing search strategies for flexible docking},
  author={Michal Vieth and Jonathan D. Hirst and Brian N. Dominy and Heidi Daigler and Charles L. Brooks},
  journal={Journal of Computational Chemistry},
We assess the efficiency of molecular dynamics (MD), Monte Carlo (MC), and genetic algorithms (GA) for docking five representative ligand–receptor complexes. All three algorithms employ a modified CHARMM‐based energy function. The algorithms are also compared with an established docking algorithm, AutoDock. The receptors are kept rigid while flexibility of ligands is permitted. To test the efficiency of the algorithms, two search spaces are used: an 11‐Å‐radius sphere and a 2.5‐Å‐radius sphere… 

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