Phyre2 vs ITasser, completely different models generated Does anyone have experience generating pdb structures with Phyre and ITasser online tools. The results generated from each given the same amino acid sequence input are very different and I am wondering whether or not this is a usual experience. I know ITasser was the number 1 rated in the CASP trails, but should the results really be this disparate?
I'm less familiar with Phyre, but I-TASSER is a really sophisticated system that takes the results of a search using multiple threaders and plugs them into an ab initio simulation which tries to minimize the energy of the models by sampling many possible 3D conformations, which I don't think Phyre does.

https://en.wikipedia.org/wiki/I-TASSER#/media/File:I-TASSER-pipeline.jpg

Compare with a similar workflow schematic for Phyre:

http://www.nature.com/nprot/journal/v10/n6/images/nprot.2015.053-F1.jpg
http://www.nature.com/nprot/journal/v10/n6/fig_tab/nprot.2015.053_F2.html

Structure prediction still has a long way to go, and you'll always get better results if there are close homologues available in the PDB, but given the consistent high performance of I-TASSER in CASP I would treat those results as more significant. That said, it can't hurt to consider multiple answers.

Edit: included blmoore's link to second half of Phyre protocol schematic