Standard Mode for job manager, batch processing, Phyre alarm and other advanced options Retrieve Phyre Job Id  
Subscribe to Phyre at Google Groups
Visit Phyre at Google Groups
 Protein Homology/analogY Recognition Engine V 2.0


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

A full 1hr45m lecture by Lawrence Kelley on protein structure prediction and how Phyre works in more detail is available:
EBI Lecture 2018

1. Söding J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21, 951-960. doi:10.1093/bioinformatics/bti125.
2. Protein Folding Requires Crowd Control in a Simulated Cell. Jefferys BR, Kelley LA and Sternberg MJE Journal of Molecular Biology (2010) Volume 397, Issue 5, 16 April 2010, Pages 1329-1338.

5796310 submissions since Feb 14 2011

Other Resources

Missense3D Portal: a suite of resources for the analysis of amino acid substitutions in proteins

GWYRE: contains modeled and experimentally determined structures of human proteins and protein complexes, annotated by phenotypic effects of genetic mutations.

Cambridge 2019 Workshop | Older Workshops | Phyre2 paper

Phyre is now FREE for commercial users!

All images and data generated by Phyre2 are free to use in any publication with acknowledgement

Accessibility Statement
Please cite: The Phyre2 web portal for protein modeling, prediction and analysis
Kelley LA et al. Nature Protocols 10, 845-858 (2015) [paper] [Citation link]
© Structural Bioinformatics Group, Imperial College, London
Michael Sternberg 
Terms and Conditions
Structural Biology Group logo Imperial logo
BBSRC logo
Phyre2 is part of Genome3D