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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: [log in to unmask] > Phone: 972-8-647-2220 Skype: boaz.shaanan > Fax: 972-8-647-2992 or 972-8-646-1710 / > // > // > / > > / > ------------------------------------------------------------------------ > *From:* CCP4 bulletin board [[log in to unmask]] on behalf of 商元 > [[log in to unmask]] > *Sent:* Sunday, December 04, 2011 2:00 PM > *To:* [log in to unmask] > *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®ards, > Yuan SHANG