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 Protein Homology/analogY Recognition Engine V 2.0

Restarting jobs from crashed nodes Mar 17 2021

After over 7 years with apparently no news, we have some!

Our current hardware is becoming increasingly unreliable, and the server nodes used appear to reboot every so often (perhaps every 2-6 weeks). A result of this is that any jobs running on a rebooting node are lost.

In order to deal with this, I am trying to develop a more robust check that will detect the crashed nodes and re-start any lost jobs. I hope this makes the user experience more pleasant.

Oh - and the other news is that, following the retirement of Lawrence Kelley, I have taken over his role. Phyre2 was Lawrence's idea over 20 years ago and he deserves considerable thanks for his ideas and work over the years.

Harry Powell

Phyre Investigator + other bits Jan 10 2014

Just released the new Phyre Investigator. Now in the table of detailed template information there is a button for each model. This button let's you submit that model for analysis by a range of methods and to view the results both in the context of the 3D structure and the sequence. I'll be adding detailed help about the system in the coming weeks. Of course this is in beta testing mode, so please let me know of any problems/suggestions you have regarding the system.

Also I've added some things to the main results page. Predicted transmembrane helices are now coloured differently, any motifs found by the Conserved Domain Database are highlighted, and the job expiry date is shown in the main results page and can be renewed with one click.

I've also made the Domain analysis and Secondary Structure sections hidden by default and all sections are now showable/hideable to make it easier to navigate and not get bogged down in too much detail.

Finally I've added help links to each section and a placeholder for video tutorials which I will be creating in the coming weeks.

I've been lax updating this news page as I tend now to post updates on twitter

OK that's all for now, and please let me know if you have any problems with the new Phyre Investigator Harry Powell

Catalytic Sites May 26 2011

I've started to incorporate the Catalytic Site Atlas into the server. At the moment, known catalytic sites in the template are highlighted in the alignment view. In the future I hope to calculate a score to indicate the likelihood of functional similarity between the query and template.

I've also now fixed the residue numbers for the template so they reflect the true residue numbers in the PDB.

Harry Powell

Model superpositions April 29 2011

I've added a new ability to select and superpose Phyre2 models so you can get an idea of where structure may be conserved or variable in your sequence. On the 'normal' results screen, under each template name are two buttons. The one on the left is a radio button so you can choose one 'master' model. The buttons on the right allow you to select a number of other models to superpose on the master. Once you've chosen your single master model and a number of other models, click on the button beneath the table. This should generate a page with a Jmol view of the superposed structures. There's more work to do in tidying it all up, but hopefully you will find it useful.

In addition I've added some help icons and tooltip info to the results page, some extra colour coding to the alignment views to highlight insertions and deletions, links to FirstGlance for extra JMol views, and extra information in the pop-ups in domain analysis. This includes % sequence identity, clarification of the PDB and chain, and the number of residues aligned and modelled. Thanks to Eric Martz for all these suggestions.

Harry Powell

Spaghetti fixed(?) and some interface tweaks April 27 2011

From looking at a range of intensive Phyre2 jobs it now looks like everything is working as planned. Phew!

After requests I've added a new section to the job manager for running jobs. This now lets you forget having to bookmark jobs running and simply go to the job manager where a list of jobs on the go are always available to monitor progress. Thanks to Dr. Mark Wass (author of 3DLigandsite) for that suggestion.

I'm also about to go live with some minor tweaks to the pop-up summaries in the domain analysis so you can see the percent i.d., aligned and modelled residues in the pop-up. Thanks to Prof. Eric Martz for those suggestions.

I am actively working through user suggestions and getting them in the server a.s.a.p.. So please don't hesitate to mail me with suggestions!

Thanks for using Phyre2

Harry Powell

Spaghetti improved and bug in One to One threading fixed April 22 2011

I've added some tweaks that should ameliorate some of the 'spaghettification' that happens occasionally with intensive mode modelling. Let me know if you get good or bad results.

I've also fixed a bug in One to One Threading caused by the presence of ANISOU records in the uploaded PDB.

More improvements to come. Don't hesitate to contact me with problems or questions. I've had a lot of people contact me recently and the server is improving all the time as a result.

Thanks for using Phyre2

Harry Powell

BackPhyre and One to One threading April 6 2011

Added functionality to BackPhyre and One to One Threading so that you don't have to extract a single chain from your PDB. Phyre2 will find the chains and ask which one you want to use - should be a bit easier.

Also I am continuing to work on preventing spaghetti in intensive mode. This is caused by two factors - 1) too much diversity in the models being used for multiple template modelling and 2) variations in relative domain orientation. I may have fixed the first issue and will be working on the second. No changes have gone live yet.

Thanks for using Phyre2 and I am keen to hear your feedback. Harry Powell

Busy busy busy March 28 2011

I have been fixing a host of small bugs. Intensive mode can't take sequences >1000 residues and I have added checks for that now.

I am still trying to fix the 'spaghetti' problem with intensive mode - its a very hard problem! Thank you for your patience. I am very keen to hear comments and criticisms from users to repair bugs and add desired functionality. Thanks.

Wiki and teething troubles with intensive mode March 16 2011

I've started a page on Phyre and Phyre2 over at Wikipedia and I will be polishing it up over the coming days

There are a bunch of tweaks I will be adding to the "intensive" mode of Phyre2 in the coming days. Under certain circumstances 'spaghetti' can be produced. I've pretty much worked out why and will be tackling this soon.

New Genome being added to BackPhyre March 16 2011

After a user request, I am adding the genome of M. tuberculosis for use in BackPhyre. Should be up within 48 hours.

Backphyre bug February 28 2011

Been fixing a range of small bugs. One is in Backphyre where jobs could run forever. Good old infinite loops. Should be fixed now.

Batch processing February 28 2011

One of our nodes collapsed but it didn't know it. So a few batch jobs had errors. I have removed the dodgy nodes and resumed these batch jobs. Batch processing will not be working properly for the rest of the day while I fix a bunch of issues. Thanks for your patience

Phyre2 is released! February 14 2011

Finally the new Phyre2 server is open for beta-testing. I am sure there will be plenty of bugs and problems in the early stages, so please let me know of anything that goes wrong, looks bad on your browser, is confusing, broken or anything you'd like changed.

I am still working on the help pages and hope to have them finished by the end of the week.

You can privately mail any issues to me below, or post on the Phyre Google group linked above. Thanks for your help.

Harry Powell

5779491 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

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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]
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