[Chimera-users] Changes in protein stability

Xhoela Bame xhoelabame at yahoo.com
Fri Dec 21 11:31:10 PST 2018

Thank you for the reply! 
I do not need many specifities. I only need to imagine what could be the change. 
Can I please have any more information or any website where I can learn the steps to perform local minimization/ count steric clashes/H bonding in Chimera?I do not know where to start from. I would highly appreciate any clue. 
Thank you! 

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On Friday, December 21, 2018, 9:59 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

Hi Kloe,
Chimera does not calculate free energies or thermodynamic stabilities, sorry.  This generally requires much more extensive modeling, such as long dynamics simulations with a dedicated package like AMBER, Gromacs, etc.  Other, more empirical programs (i.e. easier to use and shorter calculations) also exist for estimating the effects on stability of mutations, but I don’t have specific knowledge or recommendations in that area.

What you can do with Chimera is simple first-order assessments of amino acid mutations or modifications of ligands, by simply counting up H-bonds and steric clashes, or performing small local minimizations, and using your own chemical intuition. I hope this clarifies the situation,
Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 21, 2018, at 10:42 AM, kloe brathon <kloebrathon at yahoo.com> wrote:
> Dear Chimera Users,
> I am studying on a protein and its interactions with its ligands and I want to explore what would be the effect on protein thermodynamic stability if some parameters were changed such as addition, removal of hydrogen bonds or other forces. Any idea on how to do that? I am new on this. 
> Thank you on advance!
> Kloe 

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