ADL: regarding active site

Davide Mercadante dmer018 at aucklanduni.ac.nz
Fri Jun 12 15:53:01 PDT 2009


Dear Andreas,

I also thought that probably autodock found some other position on the
protein that would be more favourable for the docking of the ligand but this
is strange and not acceptable:

1) Because some other studies of docking on very similar molecules (ligands)
and the same enzyme confirm a strong affinity for these molecules in the
active site and I expected the same...using another software (DOCK) the
ligand is successful docked in the active site...

2) After the calculations the docked ligands are not in the box that I built
to perform the calculation

Something is definitively wrong. I just would like to understand what.

Please, if you or anyone in the mail-list has any suggestion I will be happy
to follow it.

Cheers,
Davide

2009/6/13 Kukol, Andreas <a.kukol at herts.ac.uk>

> You need to save the ligand after moving, with the transformed coordinates.
>
> It is possible that the ligand moved out of the binding site after docking,
> in  that case AutoDock has found a more favorable position. It should,
> however, not move outside the gridbox.
>
> Andreas
> > -----Original Message-----
> > From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu]
> On
> > Behalf Of Davide Mercadante
> > Sent: 12 June 2009 13:39
> > To: autodock at scripps.edu
> > Subject: Re: ADL: regarding active site
> >
> > Hi,
> >
> > I just did it using pmv given with autodock tools. However, the problem
> > remains because after the calculations my ligand was not there anymore.
> >
> > how to position the ligand is explained here. Here is also written that
> you
> > can only move the ligand inside a grid. This means that I have to move
> the
> > ligand in the active site just after I create the grid box?
> >
> > http://autodock.scripps.edu/faqs-help/how-to/positioning-the-ligand
> >
> > How I can solve the problem?
> >
> > Thanks,
> > Davide
> >
> > 2009/6/13 kaustubh <kaustubh.joshi at systemsbiology.fi>
> >
> > >
> > >
> > >
> > > @Davide
> > >
> > > How did you "Manually" positioned the ligand in the active site? Using
> > > AutoDock?
> > > If so please share!!
> > >
> > >
> > > Davide Mercadante wrote:
> > > >
> > > > Dear Andreas,
> > > >
> > > > actually this happened also to me. I "manually" positioned my ligand
> in
> > > > the
> > > > known active site of the enzyme and I centered the box on one atom of
> > one
> > > > of
> > > > the residues that compose the active triad of my enzyme.
> > > >
> > > > However, after the calculations, I went to visualize the
> conformations
> > > > generated but the ligand just disappeared from the active site going
> > > > somewhere else.
> > > > Please, can you help me to understand why that happened and how can I
> > > > solve
> > > > the problem?
> > > >
> > > > Thanks infintely in advance for your help.
> > > >
> > > > Best Wishes,
> > > > Davide
> > > >
> > > > Davide Mercadante - PhD student -
> > > > Department of Chemistry
> > > > Faculty of Science
> > > > The University of Auckland
> > > > Auckland 1142, New Zealand
> > > >
> > > > 2009/6/12 Kukol, Andreas <a.kukol at herts.ac.uk>
> > > >
> > > >> Use AutoDock Tools to centre the grid at a certain protein
> (receptor)
> > > >> atom
> > > >> in the binding site and then adjust the position of the gridbox
> > > manually,
> > > >> such that the centre is centered above the binding site. This works
> > very
> > > >> well, but you need to do it visually.
> > > >>
> > > >> Andreas
> > > >>
> > > >> -----------------------
> > > >>
> > > >>
> > > >> > -----Original Message-----
> > > >> > From: autodock-bounces at scripps.edu
> > > >> [mailto:autodock-bounces at scripps.edu]
> > > >> On
> > > >> > Behalf Of kaustubh
> > > >> > Sent: 12 June 2009 11:09
> > > >> > To: autodock at scripps.edu
> > > >> > Subject: ADL: regarding active site
> > > >> >
> > > >> >
> > > >> >
> > > >> > How do we specify a known active site.
> > > >> > The grid generation does not help doing so.
> > > >> > While I specify to generate grid at the ligand position, it is
> > > >> generated
> > > >> > some where at vague position and also the docking take place some
> > > where
> > > >> > else, normally at the surface of the protein.
> > > >> > This is not working out which ever way I try.
> > > >> > Anybody their to help?
> > > >> > --
> > > >> > View this message in context:
> > > >> http://n2.nabble.com/regarding-active-site-
> > > >> > tp3066853p3066853.html
> > > >> > Sent from the AutoDock mailing list archive at Nabble.com.
> > > >> >
> > > >> > ________________________________________________
> > > >> > --- ADL: AutoDock List  ---
> http://autodock.scripps.edu/mailing_list
> > > >> ---
> > > >>
> > > >> ________________________________________________
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> http://autodock.scripps.edu/mailing_list---
> > > >>
> > > > ________________________________________________
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> > > >
> > > >
> > >
> > > --
> > > View this message in context:
> > > http://n2.nabble.com/regarding-active-site-tp3066853p3067408.html
> > > Sent from the AutoDock mailing list archive at Nabble.com.
> > >
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> > >
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