How, basically, does Phyre work?
The models produced by Phyre are based on finding a sequence alignment to a known structure, copying the coordinates and relabelling the residues according to your sequence (based on the alignment). We can detect remotely homologous structures that can’t be found by conventional methods. This is because we use profiles (or PSSMs) generated by PSI-Blast for both your sequence and the sequences of the known structures. Phyre performs a profile-profile matching algorithm together with predicted secondary structure matching. The only changes Phyre makes to the backbone of the known structure (template) is when modelling insertions or deletions which is done by searching our loop library for compatible loops.
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