ADL: question about Vina vs DOCK

Kukol, Andreas a.kukol at herts.ac.uk
Fri Jun 5 08:08:35 PDT 2015


Hello David,

It is best to consider the literature for benchmarking studies of different docking programs for virtual screening. In addition it can be beneficial to combine the results from different programs. For example: this study contains a comparison of single programs (does not include DOCK6) as well as a combination of the results by different algorithms:

Kukol A. Consensus virtual screening approaches to predict protein ligands. European Journal of Medicinal Chemistry. 2011;46(9):4661-4664. Available from: 10.1016/j.ejmech.2011.05.026

Hope this helps.

Andreas


>-----Original Message-----
>From: autodock-bounces at scripps.edu [mailto:autodock-
>bounces at scripps.edu] On Behalf Of David M. Toth
>Sent: 03 June 2015 16:05
>To: autodock at scripps.edu
>Subject: ADL: question about Vina vs DOCK
>
>Hi everybody.  I was working with a chemist on virtual screening who used
>AutoDock Vina.  I'm now working with a new chemist at a different institution
>who uses DOCK6 followed by AMBER for virtual screening.  Each of the
>chemists says they use the programs they use because that's what they were
>told to by somebody more expert than themselves when they were learning to
>do virtual screening and they both seem to think their way is right.  I'm just a
>computer scientist with no chemistry background, so I haven't been able to
>figure out the answer to this myself.  Which of the two ways of doing virtual
>screening is better and why?  Given both programs are from labs with great
>reputations, there must be some major difference between Vina and DOCK or
>there wouldn't be two programs.  Can somebody please explain to me why one
>should use Vina instead of DOCK?  Thanks!
>
>Dave
>
>--------------------------------------------------
>David Toth
>Assistant Professor of Computer Science
>Centre College
>david.toth at centre.edu<mailto:david.toth at centre.edu>
>1-859-238-5405
>--------------------------------------------------
>
>________________________________________________
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