AMBER Archive (2009)

Subject: Re: [AMBER] Protein Docking

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Thu May 14 2009 - 23:28:43 CDT

Hi
 Can any one refer me to the related paper of protein-ligand docking using MD?
 Or, what is the normal method that people do on protein-ligand docking?

Thank you very much
Lin

----- Original Message -----
From: Simon Becker <simon.becker_at_uni-konstanz.de>
Date: Tuesday, May 12, 2009 8:20 am
Subject: Re: [AMBER] Protein Docking
To: AMBER Mailing List <amber_at_ambermd.org>

> Hi Lin,
>
> I had the same problem once, as I wanted to do docking starting
> from a
> x-tal structure. First I did a long equilibration run (~20 ns)
> without
> the ligand and the rmsd value stabilised over time, than steered md
> (slowly!) with the ligand. As the ligand entered the binding pocket
> the
> rmsd changed again and stabilised within 2ns of subsequent
> equilibration. So I was fairly sure everything was good.
>
> Also you could try:
> - analyse the h-bonds
> - mm_pbsa of the docking process
>
> hth
> simon
>
> steinbrt_at_rci.rutgers.edu schrieb:
> > Hi Lin,
> >
> > if your ligand-protein conformation stays close to its initial value
> > during an MD run that's a good indication (but by no means a
> proof) that
> > it is a reasonable complex geometry and good for further study.
> >
> > I would say that if you can show a stable complex rmsd during a
> > multi-nanosecond MD run, you can claim that your previous docking
> was> "successful", but there is no way besides some sort of empirical
> > verification to check that it also is correct, i.e. a complex
> geometry> occuring under physiological conditions.
> >
> > Kind Regards,
> >
> > Thomas
> >
> > On Mon, May 11, 2009 4:21 pm, Chih-Ying Lin wrote:
> >
> >> HI
> >> When i visualize the MD trajectory, the protein and ligand are
> closed by.
> >> But, I don't know if ligand really DOCK on the protein.
> >>
> >> Please tell me how to define the successful docking.
> >> Thank you
> >> Lin
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > Dr. Thomas Steinbrecher
> > BioMaps Institute
> > Rutgers University
> > 610 Taylor Rd.
> > Piscataway, NJ 08854
> >
> > _______________________________________________
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> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Simon Becker
> Dept. of Biology
> Molecular Bioinformatics
> Box M647
> Universitaet Konstanz
> D-78457 Konstanz
>
> mail: simon.becker_at_uni-konstanz.de
> Tel: 0049 7531 882900, Fax: 3183
>
>
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>

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