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

Gaokeng Xiao gkxiao at people.com.cn
Sat Feb 19 22:13:23 PST 2005


Hi everybody,
   I have some question about orientation & conformation search.

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?

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 ?

3)So if Anchor-first seaching was used,then matching could not be constrained with critical points and pharmacophe feature.   

   Best Regards,
      

 				

¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Gaokeng Xiao
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡gkxiao at people.com.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-02-20



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