Hello everyone,
I would like to calculate the energy contribution of interactions in a protein. I have the total energy of my protein but I cannot find the mean energy of interaction of a salt bridge, hydrogen bonding, a hydrophobic bond and an electrostatic bond. Does anyone could help me?
thanking you
marie
2 answers
What software have you used? I previously used FoldX (http://foldx.crg.es/) and was able to generate all the energy calculation. You can also use Foldx as YASARA plugin which gives you a visualization for what you are calculating.(http://foldxyasara.switchlab.org/index.php/FoldX_plugin_for_YASARA)
Check here for examples on how to calculate these energies: http://foldx.crg.es/examples.jsp
I used Monster. I got the number and type interaction (salt bridge, electrostatic bonding, hydrogen bonding, hydrophobic bonding) at the interface. I wonder how these interactions affect the stability of my protein.
FoldX allows me to have the total energy of the protein but I'd like to know the influence of the interface between the subunit of the protein.
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