Dec 29, 2021 · Feel free to post questions/comments/problems using Phyre2 and any additional features you would like to see.

Feb 18, 2025 · I am new to Bioinformatics and i used Phyre2 to predict secondary structure of my protein, the output is showing the % of a-helices and Beta strands, so my question is how do I get the coil %?.

Sep 3, 2021 · In short, if single sequence is searched at Phyre2 several times, each time the pocket residue will differ.

After Phyre2 is available again, it is possible that some parts of the process will not work properly straight away - please let us know by e-mail if you encounter any issues.

Aug 31, 2021 · I work on very divergent protein without entries in the PDB and I was wondering if I could use Phyre2 on custom pdb structures (obtained from modelling or ab initio predictions) ?

I've noticed that a few jobs are failing, apparently without any reason reported to the user - this is affecting about 2 or 3 jobs a day (< ~0.3% of jobs).

Oct 3, 2022 · I submitted a few sequences into Phyre2 intensive mode which are now complete but unfortunately giving me the error message ‘file not found' when I try to download the pdb file of the final model.

May 20, 2021 · The observant amongst you will have noticed that the server nodes that Phyre2 runs on occasionally reboot themselves - in spite of investigating over a period of months, none of our tech people have been able to find a cause (apart from "old age"). Mostly this doesn't cause a problem - we manage ~1000 runs a day and about once every 3 weeks one of the nodes …

I have been able to generate structures for several proteins no problem using the normal predictive model, but I am running into an issue with the One 2 One Threading. After the job "completes" there are no results. On the results page I get a " Phyre2 File not Found " error", which is attached.

I have finished modelling via online tools like Phyre2 , I-Tasser , Swiss Model and Rosetta. But cant predict the better output structure.