Solution

The default set up in the GOLD interface in CCG's MOE is designed to generate a variety of plausible and different binding poses. There are some differences from the default settings used in GOLD. These are (MOE v.s. standalone GOLD):

  • Number of GA runs: 30 v.s. 10
  • Diverse Solutions: on v.s. off
  • Flexible ligand ring corners: flip v.s. fixed
  • Ligand carboxylic OH groups: fully rotatable v.s. flip
  • Ligand pyramidal nitrogen groups: allow inversion v.s. fixed
  • Torsional distributions: not used v.s. are used
  • Relative ligand energy: off v.s. on
  • Default SF: GoldScore vs ChemPLP

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