[Dock-fans] Docking times with flexible receptor?

Scott Brozell sbrozell at scripps.edu
Tue Apr 1 13:45:19 PDT 2008


Hi,

On Wed, 12 Mar 2008, Fairchild, Steven Z. wrote:

> 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)?

300 is similar to the average number of residues in the dock protein test set
but it has only up to 7 rotatable bonds.
Dock 4 and 5 sampling times are in the range of seconds to minutes; see 
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Moustakasetal2006
12 atoms is pushing the limit of tractable sampling.

20 is similar to the average number of receptor residues within 3 to
5 Angstroms of the active site in the dock rna test set.
Amber score 5A distance movable times average about 800 seconds per ligand.

Scott




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