[gmx-users] LIE energy values for dimers

[David van der Spoel]

On 2010-03-13 20.13, jorge_quintero at ciencias.uis.edu.co wrote:
> Dear all
>
> I used LIE method in order to obtain information related with free energy
> bind between two proteins.  Previously, I obtained several dimeric
> configuration using zdock package, and geometry optimization for each
> model.  For the first ten complex, I used LIE.  These are my results:
>
> complex1 -2267.44
> complex2 -2191.92
> complex3 -2136.47
> complex4 -2430.13
> complex5 -2227.88
> complex6 -2476.61
> complex7 -2327.87
> complex8 -2219.41
> complex9 -2299.76
> complex10 -2324.9
>
> Are these value correct?.  I'll appreciate your support!
>
Impossible to say. I don't know whether there is any accepted protocol 
for this purpose, but LIE is probably too crude. There a couple of 
servers out there that will give you a value. Search for protein-protein 
interaction prediction or something like that.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se