---------- Forwarded message ---------- From: 商元 <shangyuan5...@gmail.com> Date: Wed, Dec 7, 2011 at 6:41 PM Subject: Re: [ccp4bb] Did anyone here know how to config a local protein secondary structure prediction server? To: Jose Duarte <jose.dua...@psi.ch>
Dear Jose, Thanks for you kind replies and they are very helpful. Both HSSP and consurf are based on known structures on PDB database. However, I want to scan for a certain motif, and use the conservation information as a filter to narrow down my searched results. In this case, most of these motifs exists in the linker region between domains and may not appears in the pdb database. Do you have any suggestions? Best regards, Yuan SHANG On Wed, Dec 7, 2011 at 4:31 PM, Jose Duarte <jose.dua...@psi.ch> wrote: > HSSP has it. Have a look: http://swift.cmbi.kun.nl/swift/hssp/ > > also the consurf server will give you conservation values mapped to > structure positions > > Cheers > > Jose > > > > > On 12/07/2011 09:24 AM, 商元 wrote: > > By the way, do you know any available protein database with the sequence > conservation annotation information included? > > Regards, > Yuan > > On Sun, Dec 4, 2011 at 11:32 PM, Jose Duarte <jose.dua...@psi.ch> wrote: > >> 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 * >> ** >> ** >> * >> >> * >> ------------------------------ >> *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®ards, >> Yuan SHANG >> >> >> > >
