I've seen a large number of posts from folks interested in the science behind the project. Regrettably, there is somewhat confusing vocabulary necessary to begin a discussion of the Rosetta method of protein folding, as well as comparisons of this approach with others.

I propose a brief reading list to provide a common ground from which a good discussion can begin:

Protein Structure

Protein Folding

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I propose a brief reading list to provide a common ground from which a good discussion can begin:

<li>Protein Structure
<li>Protein Folding

Thanks, this was a good idea!

I was also wondering what the purpose of the Rosetta@home project is big picture. In other words, is it to improve the usefulness/accuracy of the software itself? Is it to perform some scientific research (what kind)? Some combination of the two?

And will the results be published in peer reviewed professional journals? How will the results be disseminated?

What is the anticipated timelines (or not) for completing various phases of the project?

I guess in summary I am asking where the project is going, how long will it take to get there, and are there any milestones along the way?

Thanks!

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Regards,
Bob P.

Kel,

I liked your idea so much, as usual, I STOLE it ...

I added this start to the Wiki in the Rosetta@Home page.

And, I would have done it earlier, but I was working on deciding how to divide computer time up ... but, you will probably be happy to know that I also added Rosetta@Home to all my systems (finally) and my allocation should give this project 22% of my time ... not that it will amount to all that much ...

Almost as good of a news is that my complete "Calvin &amp; Hobbes" book came today and I may have CPDN running on the PowerMac ...

Now, if I could only get more done in the Wiki ...

=== Edit ===

Urp, are we going to develop this into something that we might want to use as intro material for Rosetta@Home?

One of my disappointments is that with all the rest of what I am doing in the Wiki I have to say the project pages seem to "lag" the most as the BOINC material is so weak everywhere ...

And I am still trying to figure out why Rosetta@Home seems to have grabbed my attention so ... weird as Bio stuff is not my usual choice ... history, computers, and particle physics (not necessarily in that order) ...

=== Edit #2 ===

I also changed Rosetta@Home to an "Active" state ... the bad news is I also moved all projects off of the first page... so you got one wish (to be active) but not the other (to be on the first page of the Wiki) ...

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I was also wondering what the purpose of the Rosetta@home project is big picture. In other words, is it to improve the usefulness/accuracy of the software itself? Is it to perform some scientific research (what kind)? Some combination of the two?

In short, Rosetta@home is an extension of the scientific efforts of the Baker lab http://www.bakerlab.org, the improvement and application of computational methods for the de novo prediction of protein structures.

While we have a relatively large number of computers in our group dedicated to Rosetta development and application (roughly 1K CPU), it is not nearly enough to tackle anything more than a subset of the interesting proteins out there. As mentioned elsewhere, it takes about 300 CPU days to produce a 'good' predicted structure for smaller proteins about 1/3 of the time. The boss, DB sees BOINC as a way to increase the computing power available to the scientists within the lab.

So, we view the BOINC project as way to both develop and apply the Rosetta algorithm. On the development front, new algorithms will be applied against standard sets and success measured against known results. On the application front, Rosetta will be applied to proteins of unknown structure - newly discovered proteins, man-man proteins, proteins yet to have been made, etc.

The goal is to be able to compute structural biology and we need/want your help to get it done.

And will the results be published in peer reviewed professional journals? How will the results be disseminated?

Absolutely. The scientific results will be published in bio-sciences journals, computational methods journals, general review journals and in other media. We will discuss the manner in which BOINC has helped push the research and, if feasible, which user provided the particular result.

We will also post successes on the website in the top predictions web page.

What is the anticipated timelines (or not) for completing various phases of the project?

This is an ongoing process. It depends upon hard work, available resources, success, insight, serendipity, stupid luck - just as on the laboratory bench.

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I liked your idea so much, as usual, I STOLE it ...

I'm sure you could do better, but I suppose it is a start...

are we going to develop this into something that we might want to use as intro material for Rosetta@Home?

Yeah, I guess my goal is to build a foundation upon which the Rosetta scientists' discussions can be fruitfully built.

I am getting ready to hound them into detailing the algorithm for this message board, but we should have a place folks can go to read up on the basics so that the descriptions make some sense. It isn't all that hard to understand what Rosetta is trying to do, but as with any speciality, the jargon can be difficult to penetrate.

I also changed Rosetta@Home to an "Active" state ... the bad news is I also moved all projects off of the first page... so you got one wish (to be active) but not the other (to be on the first page of the Wiki) ...

'you can't always get what you want....' - M. Jagger

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This is an ongoing process. It depends upon hard work, available resources, success, insight, serendipity, stupid luck - just as on the laboratory bench.

Many thanks! You guys take the award in terms of responsiveness for a BOINC project! Half the reason I participate in this project frankly is because you are all such a great group to work with!

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Regards,
Bob P.

I am getting ready to hound them into detailing the algorithm for this message board, but we should have a place folks can go to read up on the basics so that the descriptions make some sense. It isn't all that hard to understand what Rosetta is trying to do, but as with any speciality, the jargon can be difficult to penetrate.

Well, that was one of the goals of my scribbling. To try to come up with a way that we could ALL build on common ground. For example, I have an extensive glossary for the simple reason is that we do NOT have, anywhere else, a common basis for saying what does something mean in the world of BOINC.

If I error, I prefer on the side of too much ...

The other advantage is that ALL places can tie back to common grounds ...

Well, anyway, I read one of the papers, STILL don't know what it means ... I gotta go look at it again ...

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Backgrounder II, more general background....

The previous links to Wikipedia pointed to articles specific to the topic at hand, but I think even a broader background could be helpful to some. Here's a link to a general discussion of proteins that might provide some general information for folks.

Now, I've not posted these links with the idea that the contents must be memorized or even that they be read very closely. Rather, I'd imagined that folks would glance over the contents to see the pictures, get a feeling for the existance of the jargon and come away with only a general impression of things. As we discuss things we'll refer back to these documents and take a better hold of the contents.

So, here are the big-picture ideas I would 'highlight' if I were studying this for our discussion:

• "Proteins are amino acid chains that fold into unique 3-dimensional structures."
  
• "The shape into which a protein naturally folds ... is determined by its sequence of amino acids."
  
• "The mechanism of protein folding is not entirely understood."
  
• "Proteins are involved in practically every function performed by a cell...involv[ing] a protein's shape or concentration. "
  
• "Proteins are generally large molecules..."
  

Weird, huh. Big molecules that 'fold' into some 3D shape, determined by the makeup of the chain. And this 'shape' is important in all sorts of things in cells. On top of that how these molecules fold isn't too clear (I smell science!).

Let's build this introduction casually with an eye towards the enjoyment of understanding. Science is supposed to be fun afterall!

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Ok, see your words in lights, or, a Wiki ...

You can also look at this where we get started. Note that the topics in red are just candidate names ...

And, Kel, if you want to take your words into your own hands, you have but to ask ... :)

p.d.buck@comcast.net ... always on the look out for another victum in a project to add to the Wiki ...

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I wonder what the difference is between this project and Predictor@Home?

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I wonder what the difference is between this project and Predictor@Home?

https://boinc.bakerlab.org/rosetta/forum_thread.php?id=63

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Thanks, I guess I overlooked that thread... Sorry!

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