P212121

The inability of a protein to be crystallized may be due to disorder regions. A work around to this problem is to truncate the protein. The question then becomes where should these truncations be made? A number of prediction servers have been created to address this problem (Nir put together a nice list here).

The metaPrDOS (meta Protein DisOrder prediction System) is convenient in that it predicts natively disordered regions of a protein chain from its amino acid sequence by seven utilizing
independent predictors (PrDOS, DISOPRED2, DisEMBL, DISPROT (VSL2P), DISpro, IUpred and POODLE-S) (pdf: ref).

The ability of this system led to a win at CASP7. (Does anyone ever lose at CASP?)

The inputs are straight forward:

A sample output can be found here (scroll down a little). I have been waiting almost 5 hours for an output, but still no luck.

Have you used any of these prediction servers? Did you like the results? What else are you using to decide where to truncate a protein?

Related Posts:

• Extracting Structural Information from the Protein Structure Initiative
• CoFactor: The organic enzyme cofactor database
• Loops at the Protein Geometry Database
• Protein-DNA Interface Database: PDIdb
• PDB Atlas: JenaLib

5 Awesome Insights so far | Have Your Say!

1. 

   Todd
   January 19th, 2010 at 9:33 AM #

   We’ve had very good success with the FoldIndex algorithm.

   http://bip.weizmann.ac.il/fldbin/findex

   Just input your protein sequence (single letter code) and within milliseconds, you have your answer in a nice plot!

   We had such success with that algorithm that we integrated it into a sequence alignment analysis program to give averaged disorder/order predictions. It has been very useful for construct design.

2. 

   Sean
   January 19th, 2010 at 8:10 PM #

   Hi Todd,

   Thanks for the heads up! I will have to check it out.

   I still have not heard back from metaPrDOS

3. 

   Sophia
   January 21st, 2010 at 7:54 PM #

   Hi Sean,

   I tried the same today, and still nothing, 3 hours later. I tried the link above for the Weizmann FoldIndex algorithm, and it works beautifully. I like the colored sequence. (Thanks, Todd!) Seems to work well.

4. 

   Sean
   January 21st, 2010 at 7:59 PM #

   Hi Sophia,

   Yeah, I haven’t still haven’t received a reply either.

5. 

   Sophia
   January 21st, 2010 at 9:14 PM #

   Hi Sean,

   oh, guess what? After about 5 hours, I finally got something! Seems to work. You may want to resubmit. (Maybe there was a server backlog?)