[Chimera-users] Request for assistance

[Zachary W. Carpenter]

Hey Elaine,
Thanks for your quick response. Are you aware of any tutorials or wiki type
instruction guides to getting started with more complex computational
approaches to what I am describing?

Best,
Zach

On Tue, Jun 4, 2013 at 1:02 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Zachary,
> Congratulations on your recent work and publications, and thanks for your
> kind words!
>
> Chimera does not have tools for detailed prediction of changes in a
> protein's conformational ensemble or in free energy of binding or folding
> upon mutation.  Chimera tools allow first-order estimations of mutation
> impact such as loss of H-bonds or creation of steric clashes in the
> wild-type conformation or binding pocket.
>
> For more detailed calculations of a protein's energy landscape, one would
> generally perform extensive simulations with some package such as AMBER,
> GROMACS, or CHARMM (just to name a few… ).  This is computationally
> expensive and requires some expertise.  If not done well, the results can
> be useless.  Alternatively, there are less computationally intensive
> approaches that estimate the impacts of mutations with some heuristics
> and/or empirical parameter values, and these vary widely in methodology and
> accuracy.  I haven't used these myself, I only know of their existence from
> seeing various publications.  Some are even available as web servers, and
> here are just a few I found just now with web search.  (this is not an
> endorsement since I haven't used them nor studied the related publications)
>
> <http://www.ics.uci.edu/~baldig/mutation.html>
> <http://mordred.bioc.cam.ac.uk/sdm/sdm.php>
> <http://rosie.rosettacommons.org>
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Jun 4, 2013, at 8:49 AM, "Zachary W. Carpenter" <ZWC2101 at columbia.edu>
> wrote:
>
> > Dear Chimera,
> > I have been a long time user and really love your software. Recently I
> have used and cited Chimera in 4 high impact publications. One in mBio, two
> in nature medicine, and a final one in review at Nature Genetics. I have
> used Chimera to make beautiful images of mutations that we identify in NGS
> data of tumors. My role has become interpreting the effects of mutations on
> crystal structure. Thus far this has not been difficult as the effects of
> the mutations have been obvious. A recent finding however has left me
> extremely perplexed and I have need for greater accuracy of structural
> modeling of the mutations. I was wondering if you can put me in the right
> direction for creating models of mutations that are more reliable then just
> using Modeller or I-Tasser with the mutant in the sequence to be predicted.
> I know this is an elaborate question but I'd like to know which Chimera
> tools I can use to help me along this path. Or if I need to use totally new
> software/ methods.
> > Thanks for your time,
> > Zach
> >
> >
> > --
> > Zachary W. Carpenter
> > Department of Pharmacology
> > College of Physicians and Surgeons
> > Columbia University
> > 630 West 168th Street
> > New York, NY 10032
> >
> > Email: ZWC2101 at Columbia.edu
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
>


-- 
Zachary W. Carpenter
Department of Pharmacology
College of Physicians and Surgeons
Columbia University
630 West 168th Street
New York, NY 10032

Email: ZWC2101 at Columbia.edu
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