[Dock-fans] some question about DOCK's conformation search & orientation search

Terry Lang 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,
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Gaokeng Xiao
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡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
Phone:  (415)476-3986

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