[Dock-fans] some question about DOCK's conformation search
& orientation search
terry at cgl.ucsf.edu
Wed Feb 23 11:49:32 PST 2005
>1) During Anchor-First conformation search docking,the distance & node
>parameters are only used for anchor other than the whole molecule. Is it
>right? For example,if the node_minimum is set 3 & node_max is set 15,then
>at least 3 anchor's atom should match with 3 spheres' center points.This
>matching will determine the position of the anchor.And this is the
>anchor's oriention searching. Is it right?
Yes, this is correct.
>2)During rigid docking,matching is done between 3 heavy atoms of the whole
>molecule and the spheres' center. Because the whole molecule is treated as
>a anchor. Is it OK ?
This statement is technically correct. However, it is incorrect to think
of rigid docking as docking an anchor but rather docking a specific
orientation of a small molecule.
>3)So if Anchor-first seaching was used,then matching could not be
>constrained with critical points and pharmacophe feature.
This is not correct. If you are flexibly docking, you can use both
features. However, the anchor would be the only component of the molecule
that would be matched to the labeled spheres, with the substituents being
grown in after. If you have substituents that you want to match to
critical points, you have two options: 1) predefine the anchor to include
those substituents or 2) perform a conformational expansion of the ligand
and rigidly dock the conformers.
> Best Regards,
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡gkxiao at people.com.cn
>Dock-fans mailing list
>Dock-fans at docking.org
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P. Therese (Downing) Lang
Kuntz and James Labs
UCSF - CCB Graduate Program
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