ADL: Vina: does 'rigid ligand' (-Z option) re-docking success mean it's only a matter of exhaustiveness for the same ligand with torsions active?

Oleg Trott trott at scripps.edu
Mon Jul 29 15:59:15 PDT 2013


On Mon, Jul 29, 2013 at 4:30 AM, robren <RentzschR at rki.de> wrote:
> Hi again,
>
> Thanks for the reply but I think my original question is still kinda in the
> room (I do ofc know the FAQ, the paper, the principle of sampling lots of
> poses and scoring them): if I do rigid redocking of a given PDB complex, and
> the pose is native-like and gets say a -13 score, I then do the same
> redocking but with the ligand made flexible, and my top score is e.g. -8 and
> quite different from the -13 pose...wouldn't this mean it's highly likely
> the correct pose (the -13 one from the first experiment) has never been
> sampled in the flexible ligand scenario,

No. Rigid and flexible scores are not directly comparable (You can
change that by setting weight_rot = 0)

If you take your "-13" pose, make the ligand flexible without moving
it, and simply re-score it, this should give it a higher "energy" (See
Eq. 9)

-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


More information about the autodock mailing list