Re: [PyMOL] Molecule galleries

[Tsjerk W. <ts...@gm...>]

Hi,

Hear, hear! :)
A suggestion might be to pass them through the PRODRG server
(http://davapc1.bioch.dundee.ac.uk/prodrg/) which can be automated and
is capable of providing an energy minimized structure (do mind the
hydrogens/charges/valencies). It would also give you the opportunity
to provide the public with a library including topological
descriptions (in various formats) to be used for modeling. Although,
truth be told, I commonly advice against blindly using the results
from that server for modeling studies ;)

As a sidenote, it will also be more useful to have a 3D
rotatable/scalable molecule (JMol) than a fancy rendered one.

Cheers,

Tsjerk

On Thu, Sep 4, 2008 at 5:43 AM, DeLano Scientific <de...@de...> wrote:
>
> I'll second that.
>
> While applying PyMOL to generate millions of molecular renderings in an
> automated fashion may be a cool demonstration of open-source databases &
> technology, using 2D molecules as inputs kind of misses the point:
>
> PyMOL is a 3D viewer, optimized for depicting 3D representations of small
> and large molecules.  Thus I would strongly recommending passaging those
> structures through one of the open-source 2D to 3D converters before sending
> them to PyMOL for rendering.
>
> Cheers,
> Warren
>
> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of Joel Tyndall
> Sent: Wednesday, September 03, 2008 6:49 PM
> To: X-raylab info
> Cc: pym...@li...
> Subject: Re: [PyMOL] Molecule galleries
>
> Hi there,
>
> The gallery is currently in 2D format. Any plans to generate 3D galleries?
>
> J
>
> _________________________________
>
> Joel Tyndall, PhD
>
> Senior Lecturer in Medicinal Chemistry
> National School of Pharmacy
> University of Otago
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> -----Original Message-----
> From: pym...@li...
> [mailto:pym...@li...] On Behalf Of X-raylab
> info
> Sent: Thursday, 4 September 2008 3:54 a.m.
> To: x-r...@sp...
> Cc: sc...@li...; x-r...@sp...;
> o-...@or...; obj...@li...;
> co...@iu...; pym...@li...; cn...@ya...;
> gnu...@li...;
> blu...@li...; CCP4BB@JISCMAIL.AC.UK;
> gnu...@li...; cor...@iu...;
> vm...@ks...
> Subject: [PyMOL] Molecule galleries
>
>
> I have automated the process to make molecule galleries, which I am finding
> very useful to my research, so I thought that I would share the opportunity
> and take requests.  It is quick and easy.  I did a bisphenol search today,
> and as I expected, the search turned up a few stilbenes, which is the same
> molecular family as resveratrol.  Strikingly, Bisphenol A is a noted
> teratogen, which shows that care must be taken when using such molecules
> during development.  Here is a link to the bisphenol gallery.
>
> http://molecules.gnu-darwin.org/mod/Bisphenol-more.html
>
> If you would find it useful, I am definitely interested in taking
> requests for molecule galleries.   Just send me the name of your
> favorite molecule.  As you may be able to tell, we have access for galleries
> to about 1% or 0.5 million structures, in the total archive thus far, but it
> is already quite useful. The automated jobs are underway to fill in the
> rest.  The next milestone is the capability to index and make galleries for
> the remaining millions of molecules for which we have pdb files already,
> which would be 5-10% complete.  Any comments or suggestions are also
> welcome.
>
> Regards,
>
> --
> Michael L. Love Ph.D
> Department of Biophysics and Biophysical Chemistry School of Medicine Johns
> Hopkins University
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623