ADL: Cross docking

George Tzotzos gtzotzos at
Fri Mar 28 06:04:09 PDT 2008

Hi everybody,

This is a general question. I'm doing a number of cross-dockings as  
proof of concept. I find that the ligand binds where's expected to  
bind using as reference the PDB protein-ligand structure. However,  
the cluster that's closer to the reference has NOT the lowest binding  
energy. Other clusters with the ligand still in the binding pocket  
but in very different orientations give lower binding energies.

Note: I'm using very flexible ligands with 12-18 torsions (aliphatic  
hydrocarbons) with one polar group at the terminus of the molecule. I  
use 100 GA runs per job of 30 million evaluations.

Can it be that binding is non-specific? Any other suggestions  
regarding either changing the docking parameters or else?

Thanks in advance


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