DISCUSSION of Rosetta@home Journal (3)

Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3)

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milw0rm

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Message 44955 - Posted: 13 Aug 2007, 22:59:03 UTC

On 6 Jul 2007 David Baker mentioned in his journal (https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#43296) that his manuscripts were nearing completion. Could we all have a status update on this?

Thanks and best to all!
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David Baker
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Message 44980 - Posted: 15 Aug 2007, 5:48:28 UTC - in response to Message 44915.  

Hello, Dr. Baker!

I am new to Rosetta and would like to ask a question concerning DNA- cutting enzymes (endonuclease ?) that you mentioned in the journal. How do you get the enzymes into the cell nucleus? From my understanding this is the actual place where these enzymes work.
Thanks in advance,

Chris L.


good question. the designed DNA cutting enzymes will have signals attached that direct localization to the nucleus

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David Baker
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Message 44981 - Posted: 15 Aug 2007, 5:52:39 UTC - in response to Message 44955.  

On 6 Jul 2007 David Baker mentioned in his journal (https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#43296) that his manuscripts were nearing completion. Could we all have a status update on this?

Thanks and best to all!


infact, just a minute ago I finished going over the proofs of our paper on CASP7 results with rosetta@home for the journal Proteins. today we just sent back revisions on a paper describing the exciting progress on the crystallographic phase problem made using your models. and we are waiting for the proofs for Chu's manuscript on flexible protein docking using rosetta@home for JMB. within a month or two, there will be at least 5 papers available in print and online (we will post them here) based on all of your work!

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David Baker
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Message 44982 - Posted: 15 Aug 2007, 5:55:28 UTC - in response to Message 44640.  

Could you tell us more about the members of the Rosetta developers conference? From what I've heard and gathered, these are other scientists that are using/enhancing and colaborating on the Rosetta algorythm... but that is all in addition to the folks in BakerLab in Seattle?

Are these other scientific teams developing any of the techniques being used on the @home project?

Is the conference more based around the techie computer stuff? Or the bio-techie protein stuff?

How is Ian doing with the task of explaining it all? Is there a Rosetta@home home game?


this years RosettaCon was agreed by all ~100 participants (!) to have been the best ever. there were scientists from a large number of different research groups and even some visitors from the companies who license rosetta (their fees go to pay for the travel for graduate students and postdocs to rosettaCon--for example new professor Ora Furman came with two graduate students all the way from Isreal!). the science was great and many new collaborations came out of the meeting.

Ian will have a prototype game ready for you to play in a week or two!
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[AF>Linux]Arnaud
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Message 45025 - Posted: 16 Aug 2007, 6:09:36 UTC

The link to the Rotamer game doesn't exist in the last message of Dr Baker.
https://boinc.bakerlab.org/rosetta/rah_misc/king_rotamer_game/
@+
Arnaud
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Message 45029 - Posted: 16 Aug 2007, 7:32:46 UTC
Last modified: 16 Aug 2007, 7:33:49 UTC

The link to the Rotamer game doesn't exist in the last message of Dr Baker.
https://boinc.bakerlab.org/rosetta/rah_misc/king_rotamer_game/

link
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tsofka

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Message 45254 - Posted: 21 Aug 2007, 22:11:38 UTC

Now Rosetta appears to be at about 56 Teraflops and I am glad to pay the electric bill for my tiny cpu's part.

While all information regarding project is appreciated, have there been any home runs? I would love to see a list of accomplishments beyond the CASP runs put in a hall of fame or something.

Have there been any breakthroughs? It may be I just haven't found the right spot on the site.

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agge

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Message 45336 - Posted: 24 Aug 2007, 8:17:27 UTC - in response to Message 45254.  

but the results show quite contrary--the models produced are extremely accurate! this has the potential to revolutionize how scientists determine protein 3D structures using NMR data.


is this not breakthrough enough for you? i found it pretty exciting..
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Michael G.R.

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Message 45344 - Posted: 24 Aug 2007, 16:23:23 UTC - in response to Message 45336.  

but the results show quite contrary--the models produced are extremely accurate! this has the potential to revolutionize how scientists determine protein 3D structures using NMR data.


is this not breakthrough enough for you? i found it pretty exciting..


I think it's outstanding news!

And a piece about Rosetta in the WSJ would certainly bring in some new crunchers. That'd be great too.
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Profile rochester new york
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Message 45464 - Posted: 26 Aug 2007, 11:17:44 UTC - in response to Message 45344.  

but the results show quite contrary--the models produced are extremely accurate! this has the potential to revolutionize how scientists determine protein 3D structures using NMR data.


is this not breakthrough enough for you? i found it pretty exciting..


I think it's outstanding news!

And a piece about Rosetta in the WSJ would certainly bring in some new crunchers. That'd be great too.

is this what we should be looking for ref:message 45458 http://www.nature.com/nm/index.html
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Message 45472 - Posted: 26 Aug 2007, 13:50:45 UTC - in response to Message 45464.  

but the results show quite contrary--the models produced are extremely accurate! this has the potential to revolutionize how scientists determine protein 3D structures using NMR data.


is this not breakthrough enough for you? i found it pretty exciting..


I think it's outstanding news!

And a piece about Rosetta in the WSJ would certainly bring in some new crunchers. That'd be great too.

is this what we should be looking for ref:message 45458 http://www.nature.com/nm/index.html


what work units played a role in this research?
the problem is that the names don't mean anything in their raw form, so how do we know which ones went to this research?

it would be nice if there was a guide to what work units goto which research.
none the less, to get published in Nature is a good thing.
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agge

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Message 45500 - Posted: 26 Aug 2007, 23:12:07 UTC - in response to Message 45472.  

I gather Nature is quite the prestigious journal to have your work published in. Congratulations Dr. Baker.
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Message 45507 - Posted: 27 Aug 2007, 5:31:47 UTC - in response to Message 45500.  

Journal of Nature
An international journal, published weekly, with original, groundbreaking research spanning all of the scientific disciplines.

I gather Nature is quite the prestigious journal to have your work published in. Congratulations Dr. Baker.


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Ethan
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Message 45850 - Posted: 9 Sep 2007, 16:54:32 UTC
Last modified: 9 Sep 2007, 16:55:07 UTC

Here's a direct link to the journal article mentioned in DB's latest journal post:

http://www.pnas.org/cgi/reprint/0703836104v1.pdf
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Message 47536 - Posted: 9 Oct 2007, 8:08:20 UTC

We have made huge progress with the interactive video game version of rosetta. We are on our sixth trial so far, with many improvements being made at each step. in the most recent trials, a subset of the people who have tried have become hooked and played (competitively) for many hours in a row. our goal now is to increase the fraction of people who get really into the game by adding animations and other information at the beginning to help guide people starting to play for the first time.
Within the next month I will be asking for volunteers for a more general trial. The reason for all of the trials is that we want to have the game really perfect before it goes fully public. Again, the two main goals are (1) educational--I'm convinced that people playing the game will gain a huge amount of insight into what biomolecules are and how they work and (2) research--we think people playing the game may be able to find much lower energy structures than the computer working on its own. time will tell!


Would it be cheating to use PSI-BLAST, Smith-Waterman, FASTA etc.. to find probable shapes?

Never having used any of the above, I would assume that searching for either a nucleotide or protein sequance would give you the correct answer for a known protein.

On the science side, we are just completing two manuscripts describing landmarks in molecular biology: the design of novel enzymes (using computational protein design and rosetta@home) that catalyze chemcial reactions for which there are no naturally ocurring catalysts. (perhaps one of the experts among you can explain what this means on the "discussion" thread). I presented this work at two recent scientific meetings and people were pretty blown away. This opens the door to creating new catalysts for all sorts of chemical reactions that are difficult currently or require toxic or environmentally unfriendly reaction conditions.


I will leave this to someone who truly understands, as opposed to my vague concept :)

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Michael G.R.

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Message 47562 - Posted: 9 Oct 2007, 19:05:10 UTC

Has the Rosetta paper been published in *Nature* yet? If so, in which edition? Thanks.
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Message 47573 - Posted: 9 Oct 2007, 21:42:17 UTC

[...] the design of novel enzymes (using computational protein design and rosetta@home) that catalyze chemcial reactions for which there are no naturally ocurring catalysts. [...] This opens the door to creating new catalysts for all sorts of chemical reactions that are difficult currently or require toxic or environmentally unfriendly reaction conditions.


This is exceptional in two respects.

First: It has long been a dream of chemists to be able to catalyse chemical reactions in the same efficient way nature does so using enzymes. One example that illustrates it quite impressingly is the issue of nitrogen fixation. Ammonia is one of the most important raw materials in the chemical industries. It is used directly as well as indirectly, the latter mostly a nitrates, in fertilisers or as one of the major raw materials for ammunition and explosives.

If you want to make ammonia from nitrogen and hydrogen you need the so called "Haber Bosch Process", which basically means you have to heat both to 450°C (840°F) and 300 bars (4500 psi) and bring them in contact with a special catalyst. This process proved so important for agriculture (and alas also for Germany's capability of leading World War I), that Haber and Bosch got the Nobel Prize for it. A lot of plants on the other hand synthetise ammonia at ambient temperature.

Building a catalyst that can rival with what plants do (or any other life form does) would mean saving a lot of energy and thus money (and today also has a lot of value in saving the emission of lots of greenhouse gases).

Now, attempts to copy the "active sites" of proteins - the places that do the reactions - have long been made, with more or less success. If you have noticed that today you can do laundry at 40°C, well, it is due to one of these attempts. This resarch procuced a catalyst that activates the peroxy-compounds doing the bleaching and killing bacteria at considerably lower temperatures than before, when only heat could activate the release of oxygen from the peroxy compounds.

Still, many of the results achieved to date are pretty crude even if we know the exact structure of the proteins involved. So being able to produce enzymes that can do known processes very efficiently would already be a revolution in itself.

But second:

To go forth claiming to have designed a wholly new protein unmatched in nature which does a reaction that has not previously been catalysed by proteins goes right beyond this goal and out to the other side: It's a milestone on the way to true catalyst design for any reaction you like - and it has the potential to revolutionize the chemical industries.

There are so many implications that it is hard to even start describing them. Just think of processes in terms of the nitrogen fixation: faster, cleaner, safer, cheaper.
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Message 47575 - Posted: 9 Oct 2007, 22:27:07 UTC - in response to Message 47573.  

well put CJ - pinched your post and copied it here. Hope ya don't mind!

Danny
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Profile Christoph Jansen
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Message 47592 - Posted: 10 Oct 2007, 12:46:13 UTC

Something that fits exactly in here: I just heard that Gerhard Ertl receives the 2007 Nobel Prize for Chemistry. He is awarded the prize for his studies on understanding the mechanisms of chemical catalysis. Literally, the Nobel Price Committee awarded the price "for his studies of chemical processes on solid surfaces".

Industrial scale process catalysis is mostly achieved by having a solid state catalyst on which gases or liquids can react. Take your catalytic converter in your car as an example. Understanding catalysis in terms of a chain of

adsorbtion of reactants => reaction => desorbtion of products

has long been very hard to do, because it is a thing that happens on the atomic scale und is very hard to observe. So what you basically do is collect a lot of data measured on your catalyst/reactant system and try to interpret these in terms of what happens on the interface between both. By understanding known catalytic reactions researchers hope to refine important processes, but also to find possible new ones.

Now move your imagination away from this kind of "groping in the dark" approach. Imagine you would not only be able to understand cataylsis on the molecular scale, but that you can design it. Design it because you can exactly calculate which protein structure you need to synthetise a desired molecule from given reactants.

And then all you need is to produce the DNA or RNA strand that codes this protein and let bacteria or other cells produce it. As I already said in my other post, this is taking catalysis research far beyond what scientists thought they could ever do in their wildest dreams.
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Message 47594 - Posted: 10 Oct 2007, 13:10:16 UTC

Christoph, thank you very much for the detailed information in a form that we can all digest (was that pun?).

Dr. Baker has mentioned briefly in the past that in the back of his mind, an enzyme will be the solution to the increasing CO2 levels as well. Once you successfully develop such a catalyst, you probably incorporate it into a living cell such as a bateria where nature will automatically replicate it as long as a sufficient food supply remains available. The ultimate outcome might be that you sprinkle some bacteria here and there in the ocean and they absorb carbon, release (or "desorb") oxygen and then die and fall to the bottom much like organisms in nature already do.

It's probably too early to find much reading material on the subject, but please post links to any additional material on current research findings and projects that are being investigated in this groundbreaking field.
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Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
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