I contribute on both Fah and Rosie. I just read this on fah forum: (from vijay pande)

One could ask "how do you know if you understand the disease?" A good answer is new small molecule drugs which appear to prevent or minimize the effects of the disease. This too is in the works, with encouraging results in the lab (but it's not time to talk about this publicly until it passes peer review)...

I understand that a big part of the fact they've come this far may be their access to more platforms than Rosetta.

But - I'm still curious if anything like this is still way off for Rosetta?

That info is now making me invest $1700 into gear for just folding.

hi mojo

They created what I believe were the worlds first man-made enzymes (i.e. no natural pre-cursors) that actively catalysed reactions - I believe that was around a year ago(?)

There's an article here:
https://boinc.bakerlab.org/rosetta/rah_articles/Proteins_by_Design.pdf

There's also work on a HIV inhibitor for which they got a large proportion of a $10m Gates foundation grant...

If you do a quick scan of David Baker's Journal in this forum you'll see there's lots of work already been done and published by the bakerlab team.

I haven't got time to pull up the relevant info at the moment - should be asleep but watching the US election! will have a look tomorrow if no-one's added any more info.

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[q]
They created what I believe were the worlds first man-made enzymes (i.e. no natural pre-cursors) that actively catalysed reactions - I believe that was around a year ago(?)[/q]

I remember this. I don't understand what the fuss was about - there's a long way until any drugs come out of this.

Didn't find anything in the URL.

[q]There's also work on a HIV inhibitor for which they got a large proportion of a $10m Gates foundation grant...[/q]

Didn't remember this. Though it will be of no possible benefit to me unlike the AD drugs at Fah.

[q]If you do a quick scan of David Baker's Journal in this forum you'll see there's lots of work already been done and published by the bakerlab team.[/q]

I have been reading it on and off. That's the reason I ask because I don't remember reading much about any drugs there.

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[q]
They created what I believe were the worlds first man-made enzymes (i.e. no natural pre-cursors) that actively catalysed reactions - I believe that was around a year ago(?)[/q]

I remember this. I don't understand what the fuss was about - there's a long way until any drugs come out of this.

Having the ability to design drugs to catalyse a specific reaction is a massive milepost on the road to being able to design custom drugs to target specific illnesses, as well as all the other applications outside of medicine that enzyme design can offer.

An example of what that means is, for example in the case of HIV they're able to target areas of the virus that couldn't otherwise be targeted, which appears vital as the protein sheath on HIV changes so frequently. Can anyone post more details on the HIV inhibitors that were designed?

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That's the reason I ask because I don't remember reading much about any drugs there.

The main focus is on developing the tools that designer drug makers will require to cure disease.

They also designed, predicted the sturcture of, and then created a protein called Top7.

Top7, and the novel enzymes are basically labratory experiments confirming that the computer modelling is accurate.

Yes, the concrete payback is probably well in to the future. But this is the work that gets you there. Once the proteins can easily and accurately be modelled by the Rosetta program, they begin rewriting the books on medical science. They will not look at disease the same way again. They will have tools to use to knock out viruses before they kill thousands of people. Future pandemics like bird flu, and current viral invasions such as HIV, will rely on these tools to keep people safe.

Dr. Baker and his team have been working on this since before the computing power really existed to handle the problem. And they will continue working on it for many years to come.

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Rosetta Moderator: Mod.Sense

MIT's Technology Review wrote about it:

http://www.technologyreview.com/Biotech/20389/page2/

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Yes, the concrete payback is probably well in to the future. But this is the work that gets you there. Once the proteins can easily and accurately be modelled by the Rosetta program, they begin rewriting the books on medical science.

Is it possible that drug makers won't acknowledge having used Rosetta so we'll never know when it's benefited things?

Oh and about the enzymes... the reaction that was catalyzed was still much less ineffective than body's own so there's ways to go there too.

Btw, how much does Rosetta's modest computing reserve limit the work being done (1/25 that of FAH)? Maybe I should buy more quad cores instead of GPU's...

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I don't understand what the fuss was about - there's a long way until any drugs come out of this.

Potentially that will let us(humankind) to design drugs and cures for virtually any disease out there. Including things that sounds like sci-fi at the moment: cure for aging or lost limbs regeneration for example. Rosetta is a basic research, intended to solve fundamental problem that will (sooner or later) revolutionize whole medical field.

Second, don't forget that even as it is there is hundreds independent research groups all over the world who use Rosetta software to address battery of different problems. Including searches for new treatments. Rosetta is free for non-commercial use, but also good enough to be used in industry. By helping to improve it we also indirectly helping all those researches.

Folding@home is trying to address much more narrow problem and have little interest and virtually no practical use to independent researches(in comparison with Rosetta). And there is Robetta (which is itself based on Rosetta), service oriented more toward helping single scientists and small projects. And it is also very popular among scientific community.

Another way to estimate project "usefulness"/efficiency/impact is to look at scientific publications. Including how "prestigious" are publishing peer-review journals. Baker Lab also wins hands down compare to Pande Group.

And yes, Baker Lab is working on a some HIV vaccines designs. That is definitely a good thing. But I think main efforts are way more important.

I think it is a lot like Gregor Mendel, he had noticed how some peas grew larger then others, and had an idea that if he cross pollenated only larges ones with large ones, then he could make a new strain that would always be large. He did some research and found that crossing large with large did not always result in large for the next generation, so he studied further and discovered genetics, and defined how it works.

Now that we understand genetics, other researchers have used it to study plants, grow insect resistent strains of crops, and traced a number of human illnesses, traits, and ailments to your family ancestory. It really changed everything. And it changed everything in less then 100 years.

Now we look to genetics to grow more food on less land, and to understand human disease and resistence to disease. We have a tool that we can apply to the problems. It still takes time, research, and trial-and-error, but we have a tool to use to study the problem, and eventually overcome it.

So I picture Dr. Baker (and his team) as Mr. Mendel. He's out there in his garden putting funny looking baggies on pea plants (basic research), and people are walking by on the street. Some saying he's just nuts, and not giving it a second thought, (but boy did he get "lucky" with the peas on THAT plant. They're HUGE!). Others stop to ask about his idea, and how these baggies are going to help him study plant development and inheritence.

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Rosetta Moderator: Mod.Sense

Second, don't forget that even as it is there is hundreds independent research groups all over the world who use Rosetta software to address battery of different problems

You have actually read that it's been used in hundreds of research groups?

Folding@home is trying to address much more narrow problem and have little interest and virtually no practical use to independent researches(in comparison with Rosetta).

I thought that the idea was that once enough data was accumulated with FAH, other researchers would have enough to start basing other research on it.

Then I've heard although I found no mention of it on the FAH forum, that they'd have plans to simulate the function of organelles. I think that's pretty amazing.

Another way to estimate project "usefulness"/efficiency/impact is to look at scientific publications. Including how "prestigious" are publishing peer-review journals. Baker Lab also wins hands down compare to Pande Group.

I'm surprised at this too. I really thought it was the other way round.

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