Welcome to the Phyre2 Help page. Phyre2 is a major update to the original Phyre server. A range of new features have been included, accuracy has been substantially improved and the interface has been redesigned to be more intuitive and powerful.

As with Phyre, the new system is designed around the idea that you have a protein sequence/gene and want to predict its three-dimensional (3D) structure. Whereas Phyre used a profile-profile alignment algorithm, Phyre2 uses the alignment of hidden Markov models via HHsearch¹ to significantly improve accuracy of alignment and detection rate.

Phyre2 also incorporates a new ab initio folding simulation called Poing² to model regions of your proteins with no detectable homology to known structures. Poing is also used to combine multiple templates. Distance constraints from individual models are treated as linear elastic springs. Poing then synthesises your entire protein in the presence of these springs and at the same time models unconstrained regions using its physics simulation.

If you are completely new to the ideas of protein structure prediction the video below will give you a very brief overview of the general technique. More videos will be available soon from the "Video Tutorials" link above.

Full Lecture