ADL: Ice Structure

Stefano Forli forli at scripps.edu
Wed Nov 30 11:30:06 PST 2011


Hi,

by simply googling for it, I've found some potentially interesting links having PDB 
coordinates of ice:

http://www.nyu.edu/pages/mathmol/library/water/
http://www.edinformatics.com/interactive_molecules/ice.htm

You probably want to make an array of one these structures to create a surface big enough 
for your ligand (by the way, I'm curious: which kind of ligand is binding on ice?)

However, to my knowledge there isn't much about docking on ice, and energy estimations are 
assuming room temperature (298.15 K) environment.
Also, the ice surface is rather uniform with no special features, i.e. a repetition of 
Hb-acceptor/Hb-donor patterns in every direction.
That said, you want to be careful about the meaning of the results...

Happy (cold) docking,


Stefano



On 11/29/2011 07:49 PM, Nancy wrote:
> Hi All,
>
> I would like to perform molecular docking to an ice crystal surface;
> does anyone know if such a structure file can be obtained online?
>
> Thanks,
> Nancy
> ________________________________________________
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-- 
  Stefano Forli, PhD

  Research Associate
  Olson Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-112
  The Scripps Research Institute
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