I have solved a 3D structure of a protein with a ligand which seems to sit in a VERY strained conformation. I would like to quantify it by directly comparing conformational energy profile of strained vs relaxed ligand.
Is there a software I could use somewhere to perform this?
Thanks!
Dear Michal,
many thanks for asking this very interesting technical question. As an inorganic chemist I'm certainly not a proven expert in this field of research. However, I know that there are quite a few literature references about this topic available. For example, please have a look atc the following potentially useful articles:
Strain analysis of protein structures and low dimensionality of mechanical allosteric couplings
https://www.pnas.org/content/pnas/early/2016/09/20/1609462113.full.pdf
(please see attached pdf file)
and
Energy strain in three-dimensional protein structures
Article Energy strain in three-dimensional protein structures
Unfortunately the second article has not been posted as public full text on RG. However, both authors have RG profiles. Thus it should be no problem to request the full text directly from one of the authors via RG.
Good luck with your research and best wishes, Frank Edelmann
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