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Falconet
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Re: Clinical use?

I don't think Rosetta@home directly contributed to the vaccine. Rosetta@home was not credited on any of the published papers about the vaccine and the wording does not seem to indicate a *direct* contribution to the vaccine, but rather a general contribution to the development of the software and techniques. Their words:

"The computing you have provided has greatly aided in de novo protein design challenges such as vaccine development leading to breakthroughs like this."

To me, that indicates the years-long efforts to help develop and refine Rosetta. An indirect contribution. If Rosetta@home had designed the protein that was eventually developed into the vaccine, I think they would have been clearer about it and that they would have credited Rosetta@home in the papers as they usually do.
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[Edit 3 times, last edit by Falconet at Jan 19, 2024 6:13:43 PM]
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Spiderman
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Re: Clinical use?

I don't have enough information myself to state (and don't want to tie-up WCG Resources discussing another BOINC Project) -- their Twitter announcement leads one to believe the Rosetta@Home Volunteers played a key-role.

Quote:
"...The COVID-19 projects on our platform are headed into human clinical trials! Our amazing online volunteers have played a role in the development of a promising new vaccine as well as candidate antiviral treatments..."

https://twitter.com/i/status/1408533111793586178

Rosetta@Home, IPD, Baker Labs, etc, are all housed in the Univ of Washington.

And with that, I'll leave it as-is. However, Citizen Science via BOINC platforms continues to help mankind, including the Chiba Cancer Center in Japan's announcement of WCG volunteer's assistance.
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[Edit 2 times, last edit by Spiderman at Jan 20, 2024 5:37:57 PM]
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Falconet
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Re: Clinical use?

I remember that, but my questions remain. I think they are referring to the indirect contribution I mentioned. About the antivirals mentioned on that video, they said none of those came from Rosetta@home, but they acknowledge other contributions.
But you are right, this is kind of off-topic so I will leave it at that. Keep crunching!
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[Edit 1 times, last edit by Falconet at Jan 20, 2024 8:40:25 PM]
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Spiderman
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Re: Clinical use?

The main point of my comment is that Citizen Science is helping mankind and the question posed was whether any of these WU computations we do are making it into clinical use. The answer is Yes and I gave examples.

---

Regarding Rosetta that you keep bringing-up -- from the video's transcript at the link provided earlier:

"...Thank you for all of your wonderful contributions to Rosetta@Home.

We want to share with you the work that you are contributing to both in development of a COVID vaccine, an improved vaccine as well as therapeutic.

The vaccine that we've made is called a nanoparticle vaccine. And what that means is that we've taken protein and designed them so that they self assemble into larger structures that look kind of like little nanoscale soccer balls.

The reason we do this for vaccines is because if you take a from the SARS COVID two virus and you will array it on a particle like a nanoparticle, your immune system responds more strongly to it.

And that's because your immune system has evolved to detect things that are symmetric and repetitive viruses themselves are a little symmetric, repetitive arrangements of proteins. And so this turned out to be super potent in preclinical studies. And based on that work that vaccine was advanced into clinical trials.

And as long as everything looks ok there, that vaccine will be moving on to phase three and hoping that it will be licensed for use. By the end of the year, we go out into the world.

We've also been working on proteins that would directly block the virus. This would be a drug that you would get either before you might be exposed to the virus or after you've been infected.

So what we did to begin with is on Rosetta@Home, we designed hundreds of thousands of small proteins each with a unique shape.

And you can think of these, each one is like a, a potential key that could fit into the lock, which is the virus surface. So we do against the receptor binding domain. And then we redesign the amino acids at the interface to make really good interactions with the target.

It's like a key in that it matches the shape and it goes a little bit behind the key in terms of matching the chemical properties.

Now we have these things that fit perfectly against the virus.

We test them to see if they blocked the virus from infecting cells.

We've come up with proteins now that block the coronavirus from getting into cells.

And they also protect animals who have been exposed to the virus from getting sick of the things we've been doing in the last several months is developing versions of these binders with your health that neutralize all of the new variants of the virus that keep appearing.

And now we have single compounds that block all variants that have been tested.

These are now going towards Phase One clinical trials.

Moving forward where we are trying to make these methods even better and more powerful and faster. So that if there is another pandemic, we can respond even more rapidly.

So thanks again for your support..."

---

Again, Citizen Science is helping mankind. That was, and still is, my reason for posting.

Nuff said...
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Falconet
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Re: Clinical use?

I am well aware of what they said.

English is not my first language but I don't think "The computing you have provided has greatly aided in de novo protein design challenges such as vaccine development leading to breakthroughs like this" is equal to "This vaccine was designed/validated by Rosetta@home" or "The computing you provided directly led us to this vaccine". I read it as the contribution to the software over the years which is what Rosetta@home was originally created for: to help develop the Rosetta software suite.

But if Rosetta@home was indeed where the protein designs of the vaccine originally came from, why didn't they say so directly in the official vaccine announcement on the forums and why didn't they credit Rosetta@home in the research papers as they do when Rosetta@home contributes to their work?

My point about how they specifically posted on Rosetta@home that the antivirals they were developing DID NOT come from Rosetta@home also stands. And again, no credit to Rosetta@home in the research papers about those antiviral candidates.

There was something called NL-201, a cancer drug candidate. Rosetta@home was used to help validate the designs. It went as far as Phase 1 Human Clinical Trials, but these got cancelled in late 2022 (see: https://www.biospace.com/article/neoleukin-th...ovo-protein-therapeutic-/ ). We helped on that and they specifically said so back then. That was translated into real-world use.

If I didn't think Citizen Science was worth it, I wouldn't be here. Rosetta@home crunched millions and millions of work units searching for valid antiviral designs. That in and of itself was a massive, worthwhile effort that helped weed out the good and the bad, even if the antiviral protein designs that they published in their research did not come from Rosetta@home,

But they are either cryptic about the role of Rosetta@home as in the case of the vaccine, deny that any of the antivirals they published research on came from Rosetta@home, or simply don't mention Rosetta@home at all in their research articles about the vaccine and the antivirals - which is where it would matter the most.

Based on this, neither the vaccine nor the antivirals they published about came directly from Rosetta@home. As such, our computations on COVID-19 were not translated into clinical trials/practice. The vaccine, called SKYCovione, was administered in South Korea (few doses though, since it arrived at a time when many people were already vaccinated) and it was approved by the WHO for the COVAX initiative, but I don't know.how many were administered through the initiative. Recently, the manufacturer withdrew the request to have it approved in the EU. No idea if the antivirals ever started human clinical trials.

Enough said indeed. Keep crunching.

Edit: Found a post of mine raising these exact points back in 2022. https://boinc.bakerlab.org/rosetta/forum_thread.php?id=15005&postid=106166
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[Edit 4 times, last edit by Falconet at Jan 22, 2024 3:03:43 PM]
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mwroggenbuck
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Re: Clinical use?

When I started this thread, I did not intend to kick a hornet's nest. I just wanted to know if any of this computing had helped in a clinical situation, or if it was still theoretical. The answer is it has helped. Please do not argue about who or what get credit or does not. The bottom line is that our computers are helping to solve problems and having an impact on real life.

Please keep crunching! nerd
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Sgt.Joe
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Re: Clinical use?

This may be a bit off topic, but still a bit related. There is some news that a Malaria vaccine is being used in Cameroon. I don' know who developed it, how it was validated or any of the details. I do remember the short lived malaria project here. Even if the project here had nothing to do with the successful vaccine now being used, It may have provided some background on what approaches to take or not to take in the eventual successful vaccine. Knowing which avenues are dead ends in research can also provide valuable information.

Falconet: Even though English is not your native language, you write and communicate in it very well. Bravo.

Cheers
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Falconet
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Re: Clinical use?

It's not about who gets the credit, but where the work actually came from. Regardless, I'm not going to talk about Rosetta@home any more as I have said what I had to say about the subject. I will only say again that I believe in these projects, regardless of whether or not something positive is developed from them.

Thank you, Sgt. Joe. Yes, GOFAM by Dr. Perryman. It also had some work related to TB. communicated with him on Linkedin a few years back about the project. IIRC, I believe he said he managed to continue some of the research with funding from his institution, but that the TB findings from WCG were not particularly effective during lab testing due to the bacteria's fatty coating that makes it so difficult to fight. I don't recall what he said about the Malaria leads, but I know he said funding was an issue.

There was a WCG project that advanced a lot, at least based on what the project scientist told me, advanced a lot. And this was apparently confirmed by WCG when I talked to them about it (IBM era). Unfortunately, the project investigator never posted the update they said they would and did not reply to any further emails. I'll try again, I guess.
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[Edit 5 times, last edit by Falconet at Jan 22, 2024 3:14:38 PM]
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