Answers.Body: <p>This may not be the whole answer to the question, but one key difference between Phyre and ITasser (I think I'm correct in saying), is that Phyre only returns regions of the model it considers to be sufficiently well modelled, so it may not be a full length model. ITasser on the other hand, always generates full size models.</p>
  
  <p>As one of the other answers alludes to, it is very dependent on your protein of interest. If it isn't well represented in the databases, the initial threading stages will not yield good models, and the subsequent steps all suffer as a result.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-04T08:13:28.417Z
Answers.LastActivityDate: 2019-04-04T08:13:28.417Z
Answers.UserDisplayName: Joe Healey
Answers.Body: <p>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.</p>
  
  <p><a href="https://en.wikipedia.org/wiki/I-TASSER#/media/File:I-TASSER-pipeline.jpg" rel="nofollow noreferrer">https://en.wikipedia.org/wiki/I-TASSER#/media/File:I-TASSER-pipeline.jpg</a></p>
  
  <p>Compare with a similar workflow schematic for Phyre:</p>
  
  <p><a href="http://www.nature.com/nprot/journal/v10/n6/images/nprot.2015.053-F1.jpg" rel="nofollow noreferrer">http://www.nature.com/nprot/journal/v10/n6/images/nprot.2015.053-F1.jpg</a>
  <a href="http://www.nature.com/nprot/journal/v10/n6/fig_tab/nprot.2015.053_F2.html" rel="nofollow noreferrer">http://www.nature.com/nprot/journal/v10/n6/fig_tab/nprot.2015.053_F2.html</a></p>
  
  <p>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.</p>
  
  <p>Edit: included blmoore's link to second half of Phyre protocol schematic</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-05-24T13:05:21.713Z
Answers.Text: You're only linking to the first half of the phyre2 workflow: http://www.nature.com/nprot/journal/v10/n6/fig_tab/nprot.2015.053_F2.html
Answers.UserDisplayName: blmoore
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-05-20T04:11:29.220Z
Answers.LastActivityDate: 2017-05-24T18:17:03.157Z
Answers.LastEditDate: 2017-05-24T18:17:03.157Z
Answers.UserDisplayName: Rosalind Was Robbed
Body: <p>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?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-06-01T14:18:41.953Z
Comments.Text: You should always pass your models through a model quality assessment program to evaluate reliability, and select the best one.
Comments.UserDisplayName: Davidmh
Tags: <proteins><protein-structure>
Title: Phyre2 vs ITasser, completely different models generated
ThreadText: # Phyre2 vs ITasser, completely different models generated
  
  (Asked by: username_0 on 2017-05-19)
  
  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?
  
  **Tags:** proteins, protein-structure
  
  > **Comments:**
  > **username_1**: You should always pass your models through a model quality assessment program to evaluate reliability, and select the best one.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2017-05-20. Score: 5 | Accepted answer
  
  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 username_4's link to second half of Phyre protocol schematic
  
  > **Comments:**
  > **username_4**: You're only linking to the first half of the phyre2 workflow: http://www.nature.com/nprot/journal/v10/n6/fig_tab/nprot.2015.053_F2.html  
  
  ---
  
  ### Answer by username_2 on 2019-04-04. Score: 1
  
  This may not be the whole answer to the question, but one key difference between Phyre and ITasser (I think I'm correct in saying), is that Phyre only returns regions of the model it considers to be sufficiently well modelled, so it may not be a full length model. ITasser on the other hand, always generates full size models.
  
  As one of the other answers alludes to, it is very dependent on your protein of interest. If it isn't well represented in the databases, the initial threading stages will not yield good models, and the subsequent steps all suffer as a result.
  
  
  ---
  
  