Phyre2

News and updates from the developer of the protein structure prediction server Phyre2.

[Phyre2 @Phyre2server]

Sorry folks - disk failure, system down :-(

[Phyre2 @Phyre2server]

Please note new citation - "Phyre2.2: A Community Resource for Template-based Protein Structure Prediction" Powell HR et al. Journal of Molecular Biology (2025) in press DOI: https://t.co/mkTzF9Osr4

[Phyre2 @Phyre2server]

We had an internal network issue at around 5pm GMT, so some jobs failed then - apologies!

[Phyre2 @Phyre2server]

Our main machine used for starting Phyre jobs on our cluster has died (this one sits between the web-server and the cluster nodes); currently installing a replacement machine but probably no service until tomorrow (Wednesday 6th November).

[Phyre2 @Phyre2server]

It seems that the extra security offered by https will have to wait until one of our gurus is in the building next week...

[Phyre2 @Phyre2server]

We are trying to move our site from the old and insecure "HTTP" protocol to "HTTPS" today - so the server will be up and down like a yo-yo until the work is complete.

[Phyre2 @Phyre2server]

The Phyre2 server appears to be running as per spec so it should be okay to run jobs. Many thanks are due to our sys admin Suhail Islam who has been working tirelessly to get our new machine up and running. Thanks also to you all for your patience.

[Phyre2 @Phyre2server]

Hi folks - services have been down since Saturday night; we are investigating. This should be a reminder to you to let us know if you have problems accessing Phyre2 because it's very likely that no-one else has done so (first people told me just now)!

[Phyre2 @Phyre2server]

The server appears to be up but jobs are not running correctly - so please wait until the front page does not indicate any problems before submitting any new jobs. Sorry about this.

[Phyre2 @Phyre2server]

Sorry about this - there's an unidentified hardware issue, and we need to get engineers on site to investigate.

[Phyre2 @Phyre2server]

Jobs are failing for an unknown reason - maybe some hardware is about to die. Patience (and re-submission of non-batch jobs) is your friend here. For batches, please contact me by e-mail so I can try to rescue the failed jobs.

[Phyre2 @Phyre2server]

Hi - an update on this. We're having to replace the computer on which the Phyre2 server runs. The new box should be up and running by Monday 25th March 2024, but in the meantime no new jobs can be submitted and the results from old jobs cannot be accessed.

[Phyre2 @Phyre2server]

Hi folks - just noticed that the Phyre2 server is down - I don't know when it will be up again - sorry for the inconvenience

[Phyre2 @Phyre2server]

We are buying a new server rather than just upgrading the OS on the current one - so we will not be turning it off this weekend. Feel free to continue submitting jobs...

[Phyre2 @Phyre2server]

Phyre2 unavailable 1st - 4th December 2023 - server upgrade. Please don't submit big batch jobs after Thursday 30th November until Monday 4th November.

[Phyre2 @Phyre2server]

Hi folks
Sorry about this - I broke the "job description" feature in Phyre2 a couple of days ago, so any jobs will have had some kind of undefined description. If you want a useful description for your job, running the same job now should give the expected output.

[Phyre2 @Phyre2server]

Hi folks

We were wondering - in the era of AlphaFold, what are people using Phyre2 for? What features are most useful?

[Phyre2 @Phyre2server]

Sorry folks - we've had a very high load over the last few days (partly due to a software update error) so I've had to stop job submissions a couple of times. We should be back to normal in the next hour or so.