Then probably PFAM does what you want
http://pfam.sanger.ac.uk
Best
Jose
On 12/07/2011 11:43 AM, 商元 wrote:
---------- Forwarded message ----------
From: *商元* <[email protected] <mailto:[email protected]>>
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 <[email protected] <mailto:[email protected]>>
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 <[email protected]
<mailto:[email protected]>> 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 <[email protected]
<mailto:[email protected]>> 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/
<http://www.sbg.bio.ic.ac.uk/%7Ephyre/>). 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: [email protected] <mailto:[email protected]>
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710 /
//
//
/
/
------------------------------------------------------------------------
*From:* CCP4 bulletin board [[email protected]
<mailto:[email protected]>] on behalf of 商元
[[email protected] <mailto:[email protected]>]
*Sent:* Sunday, December 04, 2011 2:00 PM
*To:* [email protected] <mailto:[email protected]>
*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
