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What is the difference between the I-TASSER, phyre2, and SWISS-model in the 3D tertiary structure?

How do they get the results? When I did a prediction, I got a similar result for the highest template in I-TASSER and Swiss, while it was different with Phyre2. What does that mean?

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This is a common Q.

Briefly, you have some techniques here that get used separately or combined:

  • Ab initio: assemble the protein from scratch, often via a library fragmented peptides (3-mer, 6-mers, 9-mers) based on real structures.
  • Template threading: given a protein structure alter it to make it like a give sequence. SWISS-MODEL, Rosetta's SimpleThreadingMover, ModBase, Phyre template threading etc. This is why some of these keep ligands and deal well with multimers. For missing loops in the template these are filled by ab initio methods.
  • Hybridisation: give a bunch of models mix and match them for the best energy. I-Tasser, RosettaCM (which uses SimpleThreadingMover), Phyre (which uses Phyre template threading)
  • Ab initio with contraints, such as evolutionary covariance. EVFold, AlphaFold2, trRosetta. Often mixed with template based approaches.

Wikipedia has more, but papers are very helpful despite the car-salesmanship.

One thing to note is that protein can adopt different conformations. The AlphaFold2/ColabFold notebooks give multiple models: these may be legit alt conformations, e.g. inactive vs active etc etc

Here is a SwissModel vs AF2: Different structures of same protein from two softwares

Other helpful As:

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