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.