[Dock-fans] Flexible vs rigid ligid for docking (using DOCK 4.0)

Silberstein, Michael mikesilb at bnl.gov
Tue May 15 08:16:22 PDT 2007

I have a general question about the relationship between particular parameters and ligand flexibility in DOCK 4.0.  
First, by simply putting a 'yes' to the flexible_ligand parameter (without using anchor search), will this alone be sufficient to bring about a full conformational search to the ligand (to all rotatable bonds), or will I need to also input 'yes' to the torsion_drive parameter as well?
In other words, what does the 'yes' for flexible_ligand do?  Does that only entail a final minimization of the ligand (as long as torsion_minimize is on and torsion_drive is not on)?  Or does that entail a more expansive conformational search?  
For a more expansive conformational search for the ligand, what might you suggest as the optional set of parameters to do this?
If you can provide some feedback to me regarding these issues, that would be greatly helpful.  Thanks in advance.

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