[Dock-fans] Which one I use in DOCK

Scott Brozell sbrozell at scripps.edu
Mon Feb 4 11:43:16 PST 2008


Hi,

On Sun, 3 Feb 2008  wrote:

> Amber Score has three flavors,
>
> i) move nothing
> ii) ligand ( only move the ligand )
> iii) also move the docking site ( induced fitting )


yes where iii has many variants.

> with ii) and iii), wouldn't that be changing the coordinates and hence generating other poses?

Yes coordinates will change and so they are poses according to my
broad definition:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-February/000904.html

However, and most importantly, the control of those poses is completely
independent of DOCK's sampling algorithms. So for example, none of the uses
of scoring in anchor and grow can be performed with Amber score:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFlexibility

> or perhaps I just need to understand what you mean by rescoring poses.

In DOCK rescoring is synonymous with secondary scoring.
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Scoring
And note that again Amber score is odd since it cannot be directly
specified as a secondary score:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-December/000827.html

One technical problem with the Amber score implementation causes all
these limitations, and correcting it is on the todo list.

Scott


>  -------------- Original message ----------------------
> From: Scott Brozell <sbrozell at scripps.edu>
> >
> > On Fri, 1 Feb 2008, snoze pa wrote:
> >
> > >  I am trying to use DOCK for screening a list of ligand. I am using
> > > following tutorial
> > > http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm
> > >
> > > 1.Rigid and Flexible Ligand Docking and AMBER Score are different or  both
> > > are part of the dock process.
> > > 2. If no, then which one is better
> > >
> > > Is not clear from website which one perform better than other.
> >
> > Rigid and Flexible Ligand Docking and AMBER Score are different
> > because currently Amber score can only be used for rescoring poses,
> > not for generating poses.
> > In general, the dock process would include all five of the tutorials
> > performed in the order they are listed at the web site,
> > perhaps rescoring with a different score than Amber score.


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