metaPrDOS: Predicting Disordered Regions in Proteins
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?