[Dock-fans] joined dockfans today

[Scott Brozell]

Hi,

The input files in the tutorials
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm
are taken from actual work by Dock developers.
Start with the Structure Preparation one and continue through Amber score.
Note that Amber score is used for rescoring only at this time due to
software constraints.

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Moustakasetal2006
Note that the conformational search algorithm has been validated
for binding mode prediction on sets of ligands that have no more
than seven rotatable bonds.  In practice, 12 rotatable bonds
may be the bleeding edge now; perhaps others have comments ?

Scott

On Fri, 13 Mar 2009, Bala subramanian wrote:

> Thank you very much for the reply. Could you please give me some eg. dock.in.
> I am not getting how to use the amber score. As you know there are so many
> input parameters and it is slightly heavy for beginers like me.
> 
> I want to dock a ligand on a quadruplex DNA molecule. Can you suggest me how
> best i can do it with Dock. My ligand has lots of rotatable bonds.
> 
> On Fri, Mar 13, 2009 at 4:48 AM, Scott Brozell <sbrozell at scripps.edu> wrote:
> 
> > Hi,
> >
> > On Thu, 5 Mar 2009, Bala subramanian wrote:
> >
> > > 1) I am just staring with dock. I have the parallel dock installed in a
> > > cluster. I saw the way of running parallel dock as follows.
> > >
> > > mpirun [-machinefile machfile] [-np #_of_proc] dock6.mpi -i dock.in -o
> > > dock.out [-v]
> > >
> > > I dnt understand the term machfile. Could somebody please suggest me how
> > to
> > > generate the file.
> >
> > This is explained a couple of lines further in the manual:
> > simple text file containing the names of the computers (nodes) to be used.
> >
> > But the big picture is this:
> > The general advice for parallel DOCKing is to start with serial DOCK on a
> > small representative set of ligands. Once one has a useful serial
> > calculation then one can confidently run a large library of ligands in
> > parallel.
> >
> > > 2) Somebody please share with me your experience of using dock for
> > > nucleic-drug docking.
> >
> > We have had success reproducing experimental binding poses within 2A rmsd
> > via flexible ligand grid scoring followed by rescoring with more advanced
> > scores such as Amber score and PB/SA score.
> >