[Chimera-users] Minimized Structures vs. Unminimized

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 17 10:24:45 PDT 2020

Hi Jordan,
The minimization energy is not meant to be used quantitatively as the stability of a structure.  Minimization just goes to nearby local minimum, whereas the stability is really a free energy of a huge ensemble of structures (in solution) in folded states vs. unfolded states of the same sequence.

To summarize, if you want to figure out the relative stability of mutants, you will have to use some other program/method than Chimera.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 17, 2020, at 10:18 AM, Jordan Harriman <jnharrim at iu.edu> wrote:
> Hi there, 
> I have a protein I'm modifying, for a total of 28 unique mutations. My question is if it's possible to tell the energetic difference between a minimized structure vs. an unminimized structure. Following that, if it's possible to rank minimized structures in terms of greatest stability. Is there some quantifiable output I can use to compare structures?
> Best, 
> Jordan

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