Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server?

[Jose Duarte]

You can run psipred yourself locally by downloading the software 
available here:

http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/
You will also require blast and a local sequence database (usually 
uniref90). Have a look at the README

http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/README

This gives you a local command line application to run psipred, not a 
graphical web interface. Anyway if you really want to run a lot of 
secondary structure prediction jobs that's really what you want.

Hope this helps

Jose


Jose Duarte
Laboratory of Biomolecular Research
Paul Scherrer Institute
5232 Villigen PSI
Switzerland



On 12/04/2011 04:22 PM, Boaz Shaanan wrote:
Hi,

I would just submit your sequence to Phyre 
(http://www.sbg.bio.ic.ac.uk/~phyre/). You'll get, among other good 
things, the secondary structure predictions, perhaps even a 3-D 
structure prediction, depending on the similarity of your sequence to 
that of known structures.

           Cheers,

                      Boaz

/Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710 /
//
//
/

/
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*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 商元 
[shangyuan5...@gmail.com]
*Sent:* Sunday, December 04, 2011 2:00 PM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Did anyone here know how to config a local protein 
secondary structure prediction server?

Hi, everyone,
   I want to run plenty secondary structure prediction works and 
online prediction costs a lot of time. So I expect local software for 
secondary structure prediction will greatly help to my work.
Has anyone ever configed such local secondary structure prediction server?

Any suggestion will be welcome.

Thanks&regards,
Yuan SHANG