ADL: Autodock result analysis

L. Michel Espinoza-Fonseca mef at ddt.biochem.umn.edu
Tue Mar 25 22:09:37 PDT 2008


On Tue, Mar 25, 2008 at 11:30 PM,  <namita at ncbs.res.in> wrote:
> Hai all,

Hi Namitha,


>
>  I would like to know how to go about analysing the results of autodock.
>  The ligand in its different conformations once generated need to be
>  analysed for appropriate docking and that requires one to know the
>  interactions between the ligand and the receptor. How do we get to analyse
>  interactions in autodock?


I think the "program of choice" to analyze your results would be ADT.

>and does further analysis require use of VMD and
>  PYMOL???

The answer to this question depends on how further you want to take
your analysis. If you need to analyze your results (scoring, etc) and
the orientations of your ligands in an easy way, ADT can do a pretty
good job for you.

If you want to create pretty figures or perform some fancy analysis
(such as centroid-centroid distance calculations, RMSD, etc.), VMD can
be very helpful. Please note that I personally like VMD (partly
because I have much more experience with it than with ADT or PyMOL);
the "problem" with VMD is that you need to spend some time playing
around with it to get yourself familiar to its environment. PyMOL is
easier to use and can be used to prepare nice figures for
papers/presentations.

Cheers,
Michel

>
>  Please find time to reply to me at your earliest.
>
>  Thanks
>  Namitha Mohandas
>  National Center for Biological Sciences
>  TIFR
>  Bangalore
>  India
>
>  ________________________________________________
>  --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


More information about the autodock mailing list