How many dockings and energy evaluations should I use for each compound?Up to table of contents
This FAQ applies to: AutoDock 3
This will depend on your receptor and the computational resources available to you. One recent successful AutoDock virtual screening used 100 dockings per compound with 5,000,000 energy evaluations per docking. (Chenglong Li, Lan Xu, Dennis W. Wolan, Ian A. Wilson, and Arthur J. Olson (2004) "Virtual Screening of Human 5-Aminoimidazole-4-carboxamide Ribonucleotide Transformylase against the NCI Diversity Set by Use of AutoDock to Identify Novel Nonfolate Inhibitors" J. Med. Chem., 47: 6681-6690)
- Which values of the genetic algorithm parameters do you normally use?
- When running a docking using the GA (genetic algorithm) or LGA (Lamarckian GA), there are a number of parameters to set. Which values do you normally use?