[Dock-fans] help

John Irwin jji at cgl.ucsf.edu
Fri Apr 29 12:08:51 PDT 2005

Hi Jianing

> Hi all, I am trying to characterize the binding site 
> (ligand/protein receptor) using SPHGEN. However, when I 
> checked clusters generated by SPHGEN some parts of the ligand 
> were not covered inside the cluster, although those parts of 
> ligand binded poorly with the protein. Is this necessary to 
> manually add some clusters to cover those parts for the 
> docking?

SPHGEN generates spheres according to its algorithm. There are a few
parameters you can change, which is easy to try. We often augment SPHGEN
spheres with spheres derived from the atomic position of the ligand(s) and
even solvent molecules. If that fails, we create the spheres "by hand",
either in vi or by flying a molecule around in chimera, writing it out, and
then using its coordinates.

Hope this helps.
Good luck.

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