[Dock-fans] Should I use bump filter in my docking?

[Scott Brozell]

Hi,

On Tue, 29 Jan 2008, [gb2312] Äî Áõ wrote:

>   Thanks for dockfans' helps ,especially for Sudipto and Sahil ,my previous problem about sphgen has been resolved.

Which suggestion(s) did you ultimately employ ?

>   Now I have another problem.I have been running dock6 successfullly,but I don't know whether I should use bump filter.I run dock with rigid ligand docking.And I hope to know in which situation should I use bump filter parameter.
>    

In general, bump filtering is recommended.
However, the specifics of the active site(s) and the ligand(s)
can lead to exceptional cases, for example in sterically hindered binding.
A sensible approach is to compare and contrast rigid docking
with and without bump filtering: the spectrum of results ranges from
the highly pro-bump-filtering, where only poorly scoring poor structures
are eliminated, to the highly con-bump-filtering,
where all structures are eliminated.
See these also:
http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2006-December/000837.html
http://shoichetlab.compbio.ucsf.edu/pipermail/dock-fans/2005-May/000119.html

Scott

>   Best Regards,
>   Yolanda Guo