Paper at Science Magazine has been published and so has an article at the IPD Website.

Robetta is the public server for RoseTTAFold so it's Rosetta@home that will run jobs from researchers all over the world.

Looks like RoseTTAFold is already doing useful work - https://twitter.com/protein_artist/status/1415591642699079683

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It's really exciting stuff!

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There's an excellent article at Nature that discusses both RoseTTAFold and Alphfold 2 (Deepmind). It's non-technical and very informative .

DeepMind’s AI for protein structure is coming to the masses

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Science: Researchers unveil ‘phenomenal’ new AI for predicting protein structures
ThEy DoN't TeLl Us AnThInG

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Because Baek’s and Baker’s group has released its computer code on the web, others can improve on it; the code has been downloaded 250 times since 1 July. “Many researchers will build their own structure prediction methods upon Baker’s work,” says Jinbo Xu, a computational structural biologist at the Toyota Technological Institute at Chicago. Hassabis says its computer code is now also open source. As a result of both groups’ work, progress should now be swift, Moult says: “When there’s a breakthrough like this, 2 years later, everyone is doing it as well if not better than before.”

Thanks for the cite. If you see any of these show up on the server, let me know.
It looks like they won't need us any more, though they certainly are not telling us that.

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It looks like they won't need us any more,

I don't thins so, cause:
- these simulations needs still a lot of computational power
- these simulations is used only for one kind of simulation and not, for example, for docking

though they certainly are not telling us that.

This for sure!

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Thanks. That is more illuminating that what I have seen thus far.

When WCG/MIP shut down because they were going to AI, they gave their crunchers a month's notice.
That allowed them to migrate to other projects gracefully.

Maybe Rosetta will still have enough work, but that is not at all clear. They still have a large body of crunchers, but probably less to hand out.

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Maybe Rosetta will still have enough work, but that is not at all clear. They still have a large body of crunchers, but probably less to hand out.

From the Ars Tecnica article:

The demand for time on these systems is likely to be intense

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From the Ars Tecnica article:

The demand for time on these systems is likely to be intense

That article does not mention Rosetta.

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That article does not mention Rosetta.

But mention RoseTTAFold!! :-P

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That article does not mention Rosetta.

But mention RoseTTAFold!! :-P

Of course. And if they can run it faster on their own servers, they will. You would not send out work to BOINC unless you had to.
It involves parsing up the project into manageable pieces, and waiting several days to get results back before you can do another iteration if the next work unit depends on the previous ones.

Apparently some crunchers think that Rosetta was created to give them something to do. I don't think that is how Dr. Baker looks at it.

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That article does not mention Rosetta.

But mention RoseTTAFold!! :-P

Of course. And if they can run it faster on their own servers, they will. You would not send out work to BOINC unless you had to.
It involves parsing up the project into manageable pieces, and waiting several days to get results back before you can do another iteration if the next work unit depends on the previous ones.

Apparently some crunchers think that Rosetta was created to give them something to do. I don't think that is how Dr. Baker looks at it.

The vbox application is already pumping some tasks through, and once it's better understood I expect more researchers outside the bakerlab will start using the online submission server more too.

But my guess is that the really big amounts of compute power will be needed for protein design rather than solving existing protein structures.

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Duplicate post

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The vbox application is already pumping some tasks through, and once it's better understood I expect more researchers outside the bakerlab will start using the online submission server more too.

But my guess is that the really big amounts of compute power will be needed for protein design rather than solving existing protein structures.

I have a Ryzen 3900X with 64 GB waiting for them. Maybe they will show.
If not, I can find something else for it to do.

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I made a post in this thread and I wrote at the time that the Vbox app is TrRosetta and not RoseTTAFold - https://boinc.bakerlab.org/rosetta/forum_thread.php?id=14655&postid=102182#102182
We are already running RoseTTAFold on jobs from the Robetta server using the standard Rosetta app. I know I've had jobs on my PCs in which the "modeling method" at Robetta was RoseTTAFold - They used the Rosetta 4.20 app and Vbox wasn't used for those tasks since it's not even installed on this laptop.

I found this job at the Robetta queue- https://robetta.bakerlab.org/results.php?id=97601 - Modelling Method is RoseTTAFold.
I've also seen some jobs at Robetta that used a modeling method called "TrRefineRosetta". But I don't remember if I ran any of those - https://robetta.bakerlab.org/results.php?id=86758

All that I've seen indicates that we are running RoseTTAFold jobs using the standard Rosetta 4.20 app and we have been running those for a little while now (according to the Robetta website, RoseTTAFold has been available since the 15th of June). One of those articles on RoseTTAFold mentions that the server they set up (i.e. Robetta, IMO) had already generated more than 5000 protein structures, according to the Nature article Sean Kiely shared on this thread:

"As well as making the code for RoseTTaFold freely available, Baker’s team has set up a server into which researchers can plug a protein sequence and get a predicted structure. Since it was launched last month, the server has predicted the structure of more than 5,000 proteins submitted by around 500 people, says Baker. "

Unless I'm misunderstanding something, which is highly possible, we are indeed running RoseTTAFold using the standard Rosetta app.

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Thanks. That was not clear to me. They all looked like ordinary 4.20 Rosetta to me.

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One difference I noticed is the screensaver. The "stage" usually says fastrelax or fragmentmover or something like that but the RoseTTAFold jobs I saw had different stages, ones that I hadn't seen before at least.. I don't remember the names though.

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Apparently some crunchers think that Rosetta was created to give them something to do.

Not me.
R@H was created to make science. To make science ALSO with the help of us volunteers.
At December it's 16 years for me in this project (i started with a little single core cpu), and if i can help the research in any way (cpu, gpu, virtual machines, Foldit, etc) i'm still ready!

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Unless I'm misunderstanding something, which is highly possible, we are indeed running RoseTTAFold using the standard Rosetta app.

It would be great!

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I made a post in this thread and I wrote at the time that the Vbox app is TrRosetta and not RoseTTAFold - https://boinc.bakerlab.org/rosetta/forum_thread.php?id=14655&postid=102182#102182
We are already running RoseTTAFold on jobs from the Robetta server using the standard Rosetta app. I know I've had jobs on my PCs in which the "modeling method" at Robetta was RoseTTAFold - They used the Rosetta 4.20 app and Vbox wasn't used for those tasks since it's not even installed on this laptop.

I found this job at the Robetta queue- https://robetta.bakerlab.org/results.php?id=97601 - Modelling Method is RoseTTAFold.
I've also seen some jobs at Robetta that used a modeling method called "TrRefineRosetta". But I don't remember if I ran any of those - https://robetta.bakerlab.org/results.php?id=86758

All that I've seen indicates that we are running RoseTTAFold jobs using the standard Rosetta 4.20 app and we have been running those for a little while now (according to the Robetta website, RoseTTAFold has been available since the 15th of June). One of those articles on RoseTTAFold mentions that the server they set up (i.e. Robetta, IMO) had already generated more than 5000 protein structures, according to the Nature article Sean Kiely shared on this thread:

"As well as making the code for RoseTTaFold freely available, Baker’s team has set up a server into which researchers can plug a protein sequence and get a predicted structure. Since it was launched last month, the server has predicted the structure of more than 5,000 proteins submitted by around 500 people, says Baker. "

Unless I'm misunderstanding something, which is highly possible, we are indeed running RoseTTAFold using the standard Rosetta app.

Ah that's really interesting, but confusing - the Rosetta 4.20 application is from May 2020 according to the apps page, so it's from before any Alpahfold/AI was built into Rosetta, other than TRrosetta that was a parallel project, as I understand things. Is there any evidence that these are being pushed to R@H rather than being crunched in-house?

Or maybe they are doing the first stage (the AI bit) in-house and then we are doing the final stage which uses 4.20 on R@H, which might explain the still high volume of work coming through 4.20.

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