Hello,
I'm looking for the most easy calculation of the interaction energy between CRAC motif of protein and cholesterol. I found the paper, where is simple dockind, very short dynamics in vacuum (peptyde+cholesterol; WITHOUT LIPIDS!!) and after dynamics free Gibbs energy calculation. It has been published in one of NATURE papers. In my opinion it is to poor. Who has any idea how to calculate it simply.
Thankyou
I can't judge the Nature paper - could you give the title please?
Maybe the point was some improvements in FE calculations - as you surely know it's still a Holy Grail of biophysics :]
this is the link: http://www.nature.com/srep/2011/110819/srep00069/pdf/srep00069.pdf
and the paper in attachment
http://www.nature.com/srep/2011/110819/srep00069/pdf/srep00069.pdf
Article Disclosure of cholesterol recognition motifs in transmembran...
Calculations of proteins in vacuum are definitely not adequate. I'd tried to calculate in GB model in Amber. If this is not enough then with the explicit water and lipids, but that will not name - simply.
I agree Alexey, it should be full environment with lipid and water and minimum 100ns of seering dynamics, but it is complicated. That is why I'm looking for the easiest, acceptable way.
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