[Chimera-users] Denaturing a protein

Nadir T. Mrabet Nadir.Mrabet at univ-lorraine.fr
Fri Sep 14 11:18:54 PDT 2012

Why is that?
Simply, because the denaturate state is difficult to define as it 
certainly correspond to a multitude of conformations including some of 
the native state.

Pr. Nadir T. Mrabet
Structural & Molecular Biochemistry
N-gere - INSERM U-954
University of Lorraine, Nancy
School of Sciences and Technologies
& School of Medicine
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On 14/09/2012 19:56, Elaine Meng wrote:
> Hi Vamsee,
> Sorry no, there is no way to do those kinds of calculations in Chimera.
> Best,
> 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 Sep 13, 2012, at 6:31 PM, vamsee wrote:
>> Hi Elaine,
>> Thanks for the answer for the previous question. I am back with one more :)
>> Is there a way to completely denature a protein in Chimera? The idea is to completely unfold a particular protein (for ex: chemical denaturation GdHCl/Urea or thermal denaturation) to its primary structure. Also can this be modeled in such a way that we can extract thermodynamic parameters from the modeling? I do understand this sounds a lot like a Molecular Dynamics simulation but maybe there is a way in Chimera?
>> Thanks again
>> Vamsee
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