[Dock-fans] Using Dock for "blind-docking"

John J. Irwin jji at cgl.ucsf.edu
Thu Dec 6 14:42:03 PST 2007

Hi Ben

Thank you for your email. Sorry to take so long to get back to you.

I think is an interesting application of DOCK, and merits further study
as to whether it can be used as a general protocol. To convince a
skeptical reviewer, you would want to show that this worked on, say, 40
targets, retrospectively, and that you had not just cherry picked your
examples (i.e. only report results that work). Ideally, you would also
like to use it prospectively on at least a few targets, and show that
you were able to make a prediction that was confirmed by experiment, at
least some of the time.
> On another note - it says on your website that tutorials for "Rescoring DOCK
> Runs with Solvation Scoring Functions" and "DOCK 3.5 Scoring Functions" will
> be coming soon.  Do you have any estimation on when it will be available?  
I'm not working on it ! ;-) I think the "get version 3.5.54 features
fully into version 6" work is on hold at the moment, awaiting a new
postdoc to work on it. Thus I don't think there is a timeline, but
perhaps someone who reads this will know better.


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