Supplementary information for today's group meeting.

The following exchange was subsequent to
http://www.cgl.ucsf.edu/pipermail/chimera-dev/2002/000046.html
but just involved Eric, who forwarded it to some of us 
(at least Conrad and me, perhaps others):

From SRS0+MStz5H3d=VY=cgl.ucsf.edu=pett@cgl.ucsf.edu Wed Jul 20 11:54:37 2005
Hi Conrad,
The mail forwarded below is somewhat old, but still relevant I  
think -- something to consider for "future directions" for ViewDock.
--Eric

Begin forwarded message:
> From: "C. Klein" <cklein@pharma.anbi.ethz.ch>
> Date: September 3, 2002 10:54:08 AM PDT
> To: Eric Pettersen <pett@cgl.ucsf.edu>
> Subject: Re: [chimera-dev] congratulations to the new beta release
>
> Hi Eric,
>> Still, we're not likely to implement structure-building in Chimera.
> OK, I see. Thanks for making that clear. I can understand your
> situation. Now, chimera features that are "unique and compelling" for
> me: The first thing that comes to my mind is the interfacing with other
> public domain programs. Delphi is one example. Dock is another example.
> I have used both interfaces and find them quite useful. With all that
> hype about virtual screening, the interfacing with docking programs
> could be really useful and this could also be something which you could
> "sell" to the NIH. You currently have the dock interface... you could
> consider some more like that (autodock, gold, flexx, to name only a
> few), I think that this should not be difficult to implement. I could
> supply you with output files... One very nice feature would be consensus
> scoring -- very fashionable, and I am not sure if there is a convincing
> commercial solution (the problem is that the commercial guys do not like
> making interfaces to programs that do not originate from their own
> company, and an independent and publicly funded project has more freedom
> to be "eclectic"...).
>
> The Gold people in Cambridge (UK) are quite friendly... They have a very
> crude visualization (which runs only on SGIs....), but their docking
> program is probably the best of all. Would be neat to have a gold  
> output viewer.
>
> Consensus scoring -- that would be something great. This is also a
> medicinal chemistry application -- something for NIH. Sybyl has that
> Cscore module for consensus scoring, but I think that this module is
> unable to handle non-sybyl input (data generated by non-sybyl docking
> runs). If you could add input filters for a couple of docking programs
> and a consensus scoring functionality: would be great, and would also be
> of big interest for pharmaceutical companies.
> Best regards,
> Chris
>
Begin forwarded message:

> From: "C. Klein" <cklein@pharma.anbi.ethz.ch>
> Date: September 3, 2002 11:20:19 AM PDT
> To: Eric Pettersen <pett@cgl.ucsf.edu>
> just to make one thing more clear: I was not only talking about
> interfacing, but also about a chimera implementation of scoring
> functions (which would make consensus scoring possible). Those issues
> are related, but each one would have its own merits, independent of the
> other.  Best regards, Chris
> --
> Dr. C. Klein; cklein(at)pharma.anbi.ethz.ch
> Dept. of Applied Biosciences, Pharmaceutical Chemistry
> Swiss Federal Institute of Technology / ETH Zuerich
> Winterthurerstr. 190
> CH-8057 Zuerich
> Phone: +41 1 6356062
> FAX  : +41 1 6356884