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Frequently Asked Questions (& Answers!)

Virtual Screening

Which library should I use for virtual screening?

There are a variety of libraries that can be used for screening, which one should I use?

If you want to try and find novel compounds, you probably want to use a library designed for diversity, one which probes a large chemical space. If there are small molecules which are known to bind to your macromolecule, you may want to construct a tailored library of related compounds.

This FAQ applies to: AutoDock 3, AutoDock 4

How many dockings and energy evaluations should I use for each compound?

How much computational time should be invested in each compound?

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)

This FAQ applies to: AutoDock 3

How do I know which docking results are "hits"?

Which docking results should I consider as likely to bind well to my target?

When the results are sorted by lowest energy found for each compound, the compounds that bind as well as your positive control or better can be considered as potential hits. Remember to allow for the roughly 2.5 Kcal/mol standard error in the AutoDock scoring function. If you do not have a positive control, consider the compounds with the lowest energies as potential hits.

Note: You may also want to consider the lowest energy in the most populated cluster in your docking results, instead of the lowest energy found for all the dockings of a given compound.

This FAQ applies to: AutoDock 3, AutoDock 4

What's the best way to analyze the results?

After the virtual screening is finished, what's the best way to look at the results?

One way is to sort the compounds by lowest energy first. An alternative is to sort the compounds by the lowest energy in the largest cluster (typically clustering using an RMSD tolerance of 2 Angstroms).

Follow up the sorting by using ADT to inspect visually the chemical complementarity of the binding modes.

This FAQ applies to: AutoDock 3, AutoDock 4

Will I need to visualize the virtual screening results?

Will I need to visualize the virtual screening results?

Generally, it is wise to inspect the top 30 to 50 results. Some practitioners advocate visually inspecting the top 100-150 hits.

This FAQ applies to: AutoDock 3, AutoDock 4

How do I run virtual screening on Windows?

We have developed a virtual screening software called PyRx that can be used to run virtual screening from all major platforms, including Windows. Please visit to learn more about this software.

This FAQ applies to: AutoDock 4, AutoDock Vina

by morris last modified 2007-07-19 17:31
Contributors: Ruth Huey, Garrett M. Morris, Sargid Dallakyan, Stefano Forli

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