ADL: Docking 1byb ?

Mark Thompson mark at
Fri Jan 13 09:22:34 PST 2006

Has anyone ever tried to dock the ligand in 1byb ?
It's a beta-amylase and the ligand is maltotetraose.
I'm using the version from the Astex test set from CCDC and ArgusLab.
The ligand fit into the binding site is very snug.  I cannot get this 
ligand to dock using either a genetic algorithm or tree-pruning docking 

I'd be curious to know how Autodock handles this structure (I don't 
actually have a version of Autodock running on my machine at the present 

by the way, prior to re-docking a ligand, I scramble its torsions and 
orientation to ensure that the xray pose is  not part of the initial 
population in the GA search.

Mark Thompson
Seattle, WA
(where we have had 23 consecutive days of rain!!!....on the way to 
breaking the all time Seattle record of 33 days).

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