[Dock-fans] about GB/SA score

Terry Lang terry at cgl.ucsf.edu
Wed Jul 27 21:21:09 PDT 2005


Dear Tianlan,

There is a file in the directory /utilities/GBSA_Grids called README.
The file is a text file that contains instructions on how to run the
GBSA accessory programs and default values. Once you have run the
accessory programs, you can run DOCK with GBSA scoring. The DOCK
parameters for GBSA can be found on the web site at
http://dock.compbio.ucsf.edu/DOCK_5/DOCK_v5.2.0.htm.

Good luck and let me know if you have more questions,
Terry



tianlan7212 wrote:

> Hi dockfans:
> I'm a new user of dock5. Right now I'm using it for virtual screening
> against zinc database on a protein. After the first round of docking
> by using the energy score, 5,000 moleculars were selected from the
> database which contains nearly 50,000 moleculars. Then by using the
> contact score as a consensus score, 2,000 moleculars that had the best
> contacts with the protein were kept. However, when I want to go still
> another docking using the GB/SA score to reranking the remaining 2,000
> moleculars,the problem comes. There isn't any mannual I can find about
> how to use the GB/SA score,and how to choose the parameters to get the
> most reliable results! So could anyone kindly tell me how to use the
> GB/SA score?Thanks
> lvwei
>
>
>
>
>
> ÐèÒªÒ»¸ö2000Õ×µÄÃâ·ÑÓÊÏäÂð£¿
> ÍøÒ×Ãâ·ÑÓÊÏäÊÇÖйú×î¶àÈËʹÓõĵç×ÓÓÊÏä¡£ <http://mail.163.com>
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>
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-- 
P. Therese Lang
Kuntz and James Labs
UCSF--Chemistry and Chemical Biology
Phone: (415)476-3986

 





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