I'm not sure what to put as a heading for the latest post in the twitter feed, any suggestions?

---

Without any knowledge of previous headings on Twitter, I'm going to suggest the following:

"Fine tuning Rosetta's energy function"

---

It's been 40 days since the last update. What's going on? Working on anything new and exciting?

---

It's been 40 days since the last update. What's going on? Working on anything new and exciting?

Looks like the project team is considerably less responsive than they were back in 2006; I recently caught up on reading posts from that year.

They might be planning to add a Nvidia GPU application, and therefore attending the GPUGRID meeting in or near Barcelona, Spain. Don't expect any GPU version of minirosetta to run much faster on a GPU than on a CPU very soon, though; that would take a major rewrite to allow each GPU core to run with much less a share of memory than the current minirosetta application, even if Nvidia's plans to make more compilers available soon allow the project team to avoid rewriting the new version in an entirely different computer language.

I've already found a few articles saying that at least one copper-binding protein is very relevant to Alzheimer's research, and posted links to them in a separate thread, so there could be some resulting activity in the background.

They might be planning to add a Nvidia GPU application, and therefore attending the GPUGRID meeting in or near Barcelona, Spain. Don't expect any GPU version of minirosetta to run much faster on a GPU than on a CPU very soon, though; that would take a major rewrite to allow each GPU core to run with much less a share of memory than the current minirosetta application, even if Nvidia's plans to make more compilers available soon allow the project team to avoid rewriting the new version in an entirely different computer language.

I kind of doubt it.

From what I know, Rosetta@home takes too much RAM for current GPUs. Though I suppose that it would be possible to only run multiple instances of very small proteins on a GPU to keep the RAM requirements low while taking advantage of the many cores, but I'm not sure if such small proteins would be useful scientifically.

In any case, every time the project has been asked about GPUs they said that it's not in the plans for now.

---

I kind of doubt it.

From what I know, Rosetta@home takes too much RAM for current GPUs. Though I suppose that it would be possible to only run multiple instances of very small proteins on a GPU to keep the RAM requirements low while taking advantage of the many cores, but I'm not sure if such small proteins would be useful scientifically.

In any case, every time the project has been asked about GPUs they said that it's not in the plans for now.

Note that if they DON'T try to use all the GPU cores at once, they should have much less trouble fitting it into graphics memory. However, this idea has at least one problem: Much less speedup than if all the GPU cores could be used.

It does not, however, have a problem with proteins of the size currently handled in the CPU application.

It would, however, probably mean that my 9800 GT Nvidia card with 1 GB graphics memory would not achieve even twice the speed of the CPU minirosetta application.

So we can't quantify our progress by giving you a % complete. Instead, the project's contributions and progress can be evaluated by the many scientific publications it has produced, some of which I've tried to summarize in these posts. (the current issue of Nature for example has the article I described below on designing new enzymes to ultimately repair disease causing mutations).

Thank you for the update Dr. Baker.

Speaking of publications, this page:

https://boinc.bakerlab.org/rosetta/rah_publications.php

Doesn't include anything from 2009. Will it be updated to include the latest publications?

---

Here's a link to the (free) editor's summary of the article in "Nature" that Dr. Baker mentioned.

http://www.nature.com/nature/journal/v461/n7268/edsumm/e091029-15.html

Please note that the first author listed on the article is Summer B. Thyme, which makes me question the reliability of the judgment of certain parents.

---

excuse me if this was already posted somewhere http://online.wsj.com/article/SB10001424052748703816204574483481567116994.html

excuse me if this was already posted somewhere http://online.wsj.com/article/SB10001424052748703816204574483481567116994.html

Thanks--I hadn't seen that!

---

I sometimes get the impression that real, actual, concrete progress in medicine - and energy, for that matter - requires infinite computing power and/or infinite money, neither of which are obtainable. Since these barriers cannot be broken, progress is constrained by the level of intelligence which is in itself limited by biology (talk about irony!). But what's worse, progress in IT is not good enough all alone because all the data need to be analysed... but there is too much data for a human being or even a group of human beings. I'm pessimistic about the possibility of great or even any progress without advanced artificial intelligence.

Thank you for the update Dr. Baker.

Speaking of publications, this page:

https://boinc.bakerlab.org/rosetta/rah_publications.php

Doesn't include anything from 2009. Will it be updated to include the latest publications?

It seems like the page was updated with 2009 papers since I wrote. Thanks to whoever updated it!

---

Does this mean what I think it means?

I think we got another 'wow'.

---

Does this mean what I think it means?

I think we got another 'wow'.

Congratulations for the whole team and keep us informed! :)

Dr. Baker, can you estimate when more details will be published?

---

Hi Sean,

We are doing a series of tests and control experiments in my lab in the next 2-3 weeks to rule out various possible artifacts. If, as we expect, the design passes with flying colors, we will send it to Scripps research institute where the ability of the design to neutralize the virus in cell based tests and the extent to which the design neutralizes different strains of virus will be measured. I would expect we would know the results of this in several months. We will also work to solve the crystal structure of the design bound to the virus to confirm the design binding mode. This hopefully will not take more than a few months as well.

I will keep all of you posted in my journal about the results from these experiments. I am very optimistic, but one should be cautious about getting to excited too early about results like these--there are very many places where things can go wrong just with the biochemistry, and after this there are very many steps to actually make a protein into a drug--this is why there are so few new drugs for curing diseases being discovered.

For those of you who would like to try your hand at improving designed binders to the influenza virus, we are now posting virus inhibitor design challenges on foldit.

David

---

I am very optimistic, but one should be cautious about getting to excited too early about results like these--there are very many places where things can go wrong just with the biochemistry, and after this there are very many steps to actually make a protein into a drug--this is why there are so few new drugs for curing diseases being discovered.

Far be it for me to contradict you(!) but you did say it was an "extremely exciting result" and I kind of trust you, of all people, to be able to tell the difference between an exciting result and an "extremely" exciting result ;)

A successful drug is obviously #1, but making a step change toward an exciting result is also pretty good news and at the very worst, if it doesn't turn out successful at all, you may be able to work out just where it went 'wrong' and fine-tune your methodology.

So if it's ok with you I'll be getting a little more excited than I ought to.

Out of casual interest, has there ever been a breakthrough that's had a direct link to discoveries from a distributed computing project? Or is that too vague a question or is the process too multi-sourced for anyone to be able to point at something and say "that's when it happened"?

---

The latest news is awesome. I don't want to jump the gun and know there's a great deal of clinical trialling to be done it the binding proves successful, but getting this far is amazing.

Hopefully, this will not only be successful, but will let more people know about how they can help such research just by an install-and-forget program on their computers...

---

Still not excited? Me neither.

(I'm such a bad liar...)

Edit: Switching my resource priority even more to Rosetta.

Editx2: At what point is it worth mentioning this as news on the Rosetta front page? And does that transfer over to places like Boincstats frontpage so people get to read about something a little more important than downtime?

Little news from here gets propogated to where people might be interested to contribute more. Even if nothing comes of this, the potential for a major result is significant enough to be called real news. Don't you think?

Take a chance and do yourselves a favour - please.

---

Get a little more proactive on spreading the news and bionic users will switch.
Beats looking for noise from space! Personally SETI is a waste of power. Once we solve our problems here on earth we can then look for little green people.