[Chimera-users] Create a protein model using Chimera?
meng at cgl.ucsf.edu
Thu Oct 17 09:29:47 PDT 2013
Dear Dr Maja Divjak,
Sorry, Chimera does not do de novo modeling. Although the Chimera-Modeller interface does include untemplated loop-building, that is more appropriate for shorter missing segments within an existing protein, not entire domains or proteins.
I can only recommend you do some searching of web resources and perhaps literature, as I am sure there are many programs for that kind of modeling. I have not done it myself, so I don't have any specific recommendations. Other than that, you might try asking for recommendations of what program(s) to use on some more general forum such as the computational chemistry list, CCL.net :
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Oct 16, 2013, at 12:04 AM, Maja Divjak <divjak.m at wehi.EDU.AU> wrote:
> Hello Chimera,
> I have looked high and low for the propeptide domain of IL-1 beta, but it does not exist as a PDB. I was therefore wondering what is the best approach to generating a 3d structure for the propeptide domain using the protein sequence and Chimera? If you could please outline a possible process, I would very much appreciate it. I see you have tutorials for comparative modeling, but in this case there is nothing to compare it to except other homologous sequences from the IL-1 family.
> I look forward to your reply!
> Thank you and best wishes,
> Dr Maja Divjak,
> WEHI, Melbourne, Australia
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