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?

robren RentzschR at rki.de
Mon Jul 29 04:30:14 PDT 2013


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, including any pose within say 1A
RMSD from it that would surely get st close to -13 (even if it's not the
_exact_ same pose)? And if true, increasing exhaustiveness should at one
point lead to the pose being sampled and therefore also be the top-scoring
pose in the flexible ligand scenario?

Thanks a lot,
Rob

PS sorry for the very much delayed reply but I first had to figure out how
to use the list/nabble properly.



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