Did anyone here know how to config a local protein secondary structure prediction server?

From: 商元 <shangyuan5000


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

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From: Boaz Shaanan

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.  

 

 

                

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From: Artem Evdokimov

I highly recommend SABLE if you want to set up your own internal tool. It's pretty easy.

 

http://sable.cchmc.org/

 

Adamczak, Porollo and Meller, Proteins 56, 2004

 

SABLE uses a lot of PSI-BLAST runs, so plan your system accordingly.

 

Artem

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From: 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

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 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

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From: Jose Duarte

Then probably PFAM does what you want

http://pfam.sanger.ac.uk

Best

Jose