[Dock-fans] Docking times with flexible receptor?

[Fairchild, Steven Z.]

My group is working on a project where we would like to perform docking
simulations with both flexible ligands and flexible receptors.  It
appears DOCK 6.0 has this capability. Before installing the software, I
was hoping to get a rough idea of what the total run times are for such
simulations. 

 

As an example, suppose a person has a 300 residues protein with ~20
residues defining the active site and a ligand with ~12 heavy atoms
(all single bonds).  Roughly how long would it take to run a standard
DOCK simulation with this system (allowing both the ligand and the 20
active site residues to vary)?

 

Thank you, 

 

Steven Fairchild, Ph.D.

The MITRE Corporation

sfairchild at mitre.org <mailto:sfairchild at mitre.org> 

 

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