[Dock-fans] datdabase screening

Terry Lang terry at cgl.ucsf.edu
Tue Oct 11 17:35:14 PDT 2005


Dear Ying,

DOCK is designed to rank databases of ligands with respect to itself. It
does not calculate the absolute binding free energy. However, those
compounds with lower (more negative) DOCK scores should interact better
than those with higher (more positive) DOCK scores. This/ idea/ is true
with all of the scoring functions, but each of the scoring functions
have different accuracy rates and different lengths of time for the
calculation.

Sincerely,
Terry


ying xiong wrote:

>Dear sir,		
>   I am a new use for DOCK. I see in the web that we can use DOCK for the following applications:"       
>search databases of ligands for compounds that inhibit enzyme activity, search databases of ligands for compounds that bind a particular protein."
>   Now if I dock many small molecules to a protein with DOCk program, I don't know what's the criterion for screening those molecules which can bind a protein or have a high activity.
>   In DOCK program, which energy score can correspond to binding free energy? 
>
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡ying xiong
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡yxiong99 at 163.com
>¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2005-10-11
>
>
>
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>  
>

-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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