B-P.08: Phyre2.2: A web server to predict protein structure and protein/ligand complexes
Harold R Powell
Imperial College London
Eleanor Stevens
Imperial College London
Anja Conev
Imperial College London
Suhail A Islam
Imperial College London
Alessia David
Imperial College London
Michael J E Sternberg
Imperial College London
Keywords
homology modelling, protein structure, molecular docking, cofolding
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Template-based protein structure prediction remains a powerful complementary approach to the recent machine-learning algorithms such as AlphaFold and Boltz. Indeed, our Phyre server continues to be widely used with over 30,000 unique users running over 200,000 jobs in 2025.
Our new release, Phyre2.2, enables a user to input a sequence and the program then identifies the closest AlphaFold2 model which then acts as a template for model prediction. This is in addition to the traditional Phyre2 approach of basing the model on an experimental Protein Data Bank (PDB) structure. Using an AlphaFold structure as a template will be particularly useful when a new proteome has been sequenced and models are not yet available to the community.
We are also launching Phyre2.2 Ligand which enables a user to obtain a model for a ligand located within a Phyre2.2 predicted structure. There are two modes for Phyre2.2 Ligand. In both, the first step cavities are identified in the predicted structure. Then, in the first mode, the coordinates of a ligand in the template are transplanted into the predicted model to generate a downloadable protein/ligand complex. In the second mode Phyre2.2 ligand will enable a user to dock a selected ligand into the predicted structure using AutoDock Vina. The ligand can be from the PDB template, from a UniProt entry or user defined via a SMILE string.
Phyre2.2, an ELIXIR resource, is freely available to all users, including commercial users, at https://www.sbg.bio.ic.ac.uk/phyre2/ .
Co-authors: Harold R Powell, Suhail Islam, Eleanor Stevens, Alessia David, Michael Sternberg
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