DISCUSSION of Rosetta@home Journal (3)

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

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David Baker
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Message 32393 - Posted: 10 Dec 2006, 8:44:05 UTC - in response to Message 32387.  

What is the differens between the "Baker" and "Zhang" ways of solving

a Casp 7 targets.

And are there something for Rosetta to learn from

how other teams have solved the tasks in Casp 7?

Anders n



Good question. There are two sources of information which protein structure prediction can draw on: evolution and physics. Zhang's approach is excellent at using all evolutionary information available from related protein structures, wheras our search for the global energy minimum uses physical chemistry information. As you suggest, the two approaches are quite complementary and we can each learn from each other. I invited Zhang to the University of Washington last month for a seminar, and we spent an excellent day discussing routes for collaborating, and we are currently exchanging datasets and programs. Using evolutionary information will help us narrow down the part of the space that needs to be searched so that we can better focus your searches on areas where the global energy minimum (correct structure) is likely to be, and thus improve prediction of larger more complex protein structures.
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Message 32415 - Posted: 10 Dec 2006, 18:22:18 UTC

congrats to everyone at the bakerlab! ;)
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BennyRop

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Message 32831 - Posted: 18 Dec 2006, 0:34:25 UTC

This is impressive praise.. that Rosetta is ready for predicting native configurations against the labor intensive techniques currently used. What was different between the predictions where we were in the middle of the pack on the predictions and the ones where we were at the head of the pack?

Here's looking forward to further improvements - that will hopefully reduce the workload and get more of our results closer to the neighborhood of the winning results.
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David Baker
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Message 33743 - Posted: 30 Dec 2006, 7:22:16 UTC - in response to Message 32831.  

This is impressive praise.. that Rosetta is ready for predicting native configurations against the labor intensive techniques currently used. What was different between the predictions where we were in the middle of the pack on the predictions and the ones where we were at the head of the pack?

Here's looking forward to further improvements - that will hopefully reduce the workload and get more of our results closer to the neighborhood of the winning results.



For the most part, we did better on the proteins less than 200 amino acids--even with all of your help the larger proteins were still difficult to search in the roughly day of computer time we had for each.. however, there were still some smaller proteins we think we could have done a lot better on, and we are currently working on techniques to improve prediction of this class of problems--some of the rosetta@home jobs currently running are testing these methods improvements.

I am now trying to spread the word among NIH officials and scientists working on X-ray crystallography that our high resolution refinement methods together with rosetta@home can be broadly useful for speeding up X-ray structure determination, which the NIH is very heavily investing in currently. the examples from CASP7 are really stunning, and now we want more problems where the structure has not been solved at all to show the new methods, and your efforts, can do amazing things.
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Message 34123 - Posted: 4 Jan 2007, 22:21:10 UTC
Last modified: 4 Jan 2007, 22:21:51 UTC

In another news, I just put the final touches on the paper describing the first round of results from the rosetta WCG project led by my former graduate student Richard Bonneau who is now a professor at NYU


Hi, thanks for the report. I am a little puzzled with the "rosetta WCG" part though ..

Does is it mean it will describe results obtained from rosetta .. or from HPF2?(WCG). or are they the same thing anyway?..(the science behind them - that is).


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Message 34130 - Posted: 4 Jan 2007, 23:17:43 UTC

Bakerlab works to make Rosetta work better. WCG is using what they've got so far and applying the tool to specific proteins and diseases. Rosetta is a tool, like a microscope. Bakerlab works to bring better focus on the objects studied, and to allow you to see them with less light. WCG is using the best Baker "microscope" available to study the things they stick under it.

So, in that sentence, Dr. Baker is referring to the Rosetta program... not the Rosetta@home project specifically.
Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/
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Message 34155 - Posted: 5 Jan 2007, 10:59:51 UTC - in response to Message 34123.  

[/quote]

Hi, thanks for the report. I am a little puzzled with the "rosetta WCG" part though ..

Does is it mean it will describe results obtained from rosetta .. or from HPF2?(WCG). or are they the same thing anyway?..(the science behind them - that is).

[/quote]

What Dr. Baker is referring to in "Rosetta WCG" is the HPF1 project recently completed on the IBM World Community Grid. It used a version of Baker Labs Rosseta Program that was about 2 years old to survey 150 Genomes (including the Human Genome).
This survey was done in low resolution mode and the results were used to create a public database which show the results of the many protien structure predications from the genome sequences.

The HPF2 project takes a subset of the most interesting predictions from HPF1 and does a hig resolution prediction on these. HPF2 is using the most current stable version of Rosseta to do the high resolution prediction. I belive the newest version came from the work of rosetta@home. The version used on HPF1 predates the rosseta@home project.


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Profile Faust

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Message 34156 - Posted: 5 Jan 2007, 11:22:02 UTC

Thanks Bruce and Feet1st, all clear now.

am doing 50%-50% with rosetta and WCG now. still waiting to HPF2 to resume on BOINC though.


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Message 34193 - Posted: 6 Jan 2007, 4:51:30 UTC

rosetta Yeah!
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Markus Zeller

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Message 36149 - Posted: 5 Feb 2007, 11:29:37 UTC - in response to Message 36140.  

We are just finalizing two manuscripts which describe some of the most exciting results obtained thus far by rosetta@home. We have identified the rosetta@home contributors who found the rather spectacular low energy structures reported in the first paper, and would like to acknowledge them in the paper. Our question is whether to acknowledge these contributions through usernames or real names, and we certainly don't want to use the latter without permission. Here are the user names of the four participants for the first paper, I'll post the participants we would like to acknowledge in the second paper when we have identified them.

78884 aotama
66651 DJ N-4ceR
77194 DOJ F@T Elvis Clan
49841 Vroomfondel

It would be great if the above participants could let us know how they would like to be acknowledged.


Hi there!

Thank you Ethan for taking the time contacting me. As I can see you were asking for my real name.

>> 66651 DJ N-4ceR <<

My name is Markus Zeller, Stated in Dortmund, Germany.
http://www.n4cer.de

Thank you in advance!


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FluffyChicken
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Message 36170 - Posted: 5 Feb 2007, 18:58:22 UTC - in response to Message 36140.  

We are just finalizing two manuscripts which describe some of the most exciting results obtained thus far by rosetta@home. We have identified the rosetta@home contributors who found the rather spectacular low energy structures reported in the first paper, and would like to acknowledge them in the paper. Our question is whether to acknowledge these contributions through usernames or real names, and we certainly don't want to use the latter without permission. Here are the user names of the four participants for the first paper, I'll post the participants we would like to acknowledge in the second paper when we have identified them.

78884 aotama
66651 DJ N-4ceR
77194 DOJ F@T Elvis Clan
49841 Vroomfondel

It would be great if the above participants could let us know how they would like to be acknowledged.



David, could you double and triple check the peopl since

Vroomfondel https://boinc.bakerlab.org/show_user.php?userid=49841 has NO RAC and NO CREDIT Joined and last contact was at the same time, so I'm guessing actually did no work whatsoever ?
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Rhiju
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Message 36172 - Posted: 5 Feb 2007, 19:35:14 UTC - in response to Message 36170.  

Hi FluffyChicken:

You're right, instead of vroomfondel (49841), it should have been:

49481 S-A-M

I've double-checked the other users. Thanks! Great eye! I'll ask David to correct his post (and maybe move these posts to the commentary on the journal).
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Ethan
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Message 36173 - Posted: 5 Feb 2007, 19:43:36 UTC - in response to Message 36172.  

I moved the previous three messages to this thread from DB's Journal.
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Message 36196 - Posted: 6 Feb 2007, 10:26:05 UTC

Is it possible to put the teamname after the username?
Not everyone, who crunches for Rosetta, do read the messageboards actively.
If someone sees a person from the same team, he can easely warn him on internal messageboards or other methods...
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FluffyChicken
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Message 36212 - Posted: 6 Feb 2007, 19:09:28 UTC
Last modified: 6 Feb 2007, 19:25:19 UTC

That's how I noticed the error above, i was checking to see if there was any teams I knew.

Here you go.

TechIMO (Jynxedu)

---

Serbia - The Wild Bunch (Marko)
Team Downham (UK) (Ian_D)
Poland Null_Zero Team (pxee)
Seti.Germany (csbyrosetta)

---

Arizona State University (TJSwan)

---

UK BOINC Team (UBT - Menace)

---

Seti.USA (D. Brown)

---

danish team (Bjarke.Orbeck)
Russia Team (SerVal)
Dutch Power Cows (Erik)

---

Dutch Power Cows ([DPC]FOKschaap~devzero)
Team Art Bell (A's Team)
Boinc@Austria (jeidler)
TeAm AnandTech (Rebel Alliance)


everyone else is a member of the exclusive Team None ;-)
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Message 36231 - Posted: 7 Feb 2007, 3:09:54 UTC

Adam, Richard, and Mike P have the only machines currently crunching Rosetta for the Rebel Alliance that I am aware of. ( Mike P is a coworker of mine who has Rosey running on a couple of machines for us )

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Keith Akins

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Message 36643 - Posted: 13 Feb 2007, 7:48:55 UTC

Dr. Baker's jounal entries from 2007 seem to be missing. Maybe they got achived. I know there were three entries from 2007 that I can't seem to find.
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FluffyChicken
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Message 36647 - Posted: 13 Feb 2007, 8:13:45 UTC - in response to Message 36643.  

Dr. Baker's jounal entries from 2007 seem to be missing. Maybe they got achived. I know there were three entries from 2007 that I can't seem to find.

5 entries and still there
https://boinc.bakerlab.org/forum_thread.php?id=1177

Check the bottom/top depending on your forum preferences (for me they are at the bottom)
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Message 36658 - Posted: 13 Feb 2007, 14:01:15 UTC

Keith, none of Dr. Baker's journal entries have been deleted. Especially none that recent. Perhaps you have your message board preferences set to only display a small number of messages per page? In that case, there is a link at the bottom of your list to show the additional messages. Then at the "bottom" of the journal thread there is a link to another thread where we've placed all of his older entries.
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Message 36839 - Posted: 15 Feb 2007, 12:45:53 UTC

David,

Can't you send an e-mail to these contributors?

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



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