DISCUSSION of Rosetta@home Journal (3)

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Message 31428 - Posted: 19 Nov 2006, 18:55:45 UTC

This thread is the third of a series where participants can discuss and ask questions about Dr. Baker\'s journal entries.

To reference discussions prior to this, see Discussion 2.
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Message 31510 - Posted: 21 Nov 2006, 13:15:54 UTC - in response to Message 31428.  

After the CASP meeting, will we then start the folding and design of proteins to fight diseases? Or when is it planned to be done?

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Message 31515 - Posted: 21 Nov 2006, 15:40:30 UTC - in response to Message 31510.  

After the CASP meeting, will we then start the folding and design of proteins to fight diseases? Or when is it planned to be done?


We have been doing this since CASP ended Aug 1! Your computers have worked on refining HIV vaccines and building models of the Alzheimer\'s fibril in the last months, among other disease related projects.
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Message 31518 - Posted: 21 Nov 2006, 16:19:23 UTC - in response to Message 31515.  
Last modified: 21 Nov 2006, 16:20:08 UTC

After the CASP meeting, will we then start the folding and design of proteins to fight diseases? Or when is it planned to be done?


We have been doing this since CASP ended Aug 1! Your computers have worked on refining HIV vaccines and building models of the Alzheimer\'s fibril in the last months, among other disease related projects.


Thanks for your answer.
I check the Boinc graphics once in a while and I saw only once a HIV WU, the rest were test WUs for a better prediction method (at least that\'s what it said).
Now I know that I can increase my contribution and RAC again to about 800-900 as it used to be before I concluded (after CASP was over) that we were only testing and testing for months.

Thanks again!
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Message 31895 - Posted: 1 Dec 2006, 10:07:23 UTC

I\'m just back from the CASP7 meeting which was very exciting. I will give a fuller report this weekend after I catch up on sleep and the pile of things which has accumulated, but very briefly it turns out that many of the predictions Rhiju and Bin have posted on the \"top predictions\" page were the best made for these targets in the whole prediction experiment, and for the experts among you, the T283 ab initio prediction was found by the CASP7 assessor to be accurate enough to unambigously solve (by molecular replacement) the xray crystallography phase problem, an absolutely unprecedented result.


That\'s fantastic news!

The graphs are here for anyone that hasn\'t seen them (the Bakerlab submissions are the black lines).
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Message 31896 - Posted: 1 Dec 2006, 10:48:23 UTC

Nice, but can someone give some more info for a person who doesn\'t know anything about this medical/theoretical/science/... :)
I take for example this one.
I see the black curve on the right. Is this good? What is (theoretical) the best solution? How good is the prediction of Baker comparable to the other ones?


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Message 31900 - Posted: 1 Dec 2006, 14:15:54 UTC

That is already done in this topic

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Message 31928 - Posted: 2 Dec 2006, 5:09:33 UTC

Here\'s a direct link to the HHMI article about Rosetta. This is the article by Lindsay Moran discussed here.
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Message 31964 - Posted: 2 Dec 2006, 20:22:28 UTC - in response to Message 31923.  

I\'ll post more soon on the CASP7 results--for now you can view all of the numerical evaluation of the predictions at the CASP7 web site. The human expert evaluations will be posted there soon as well.

I just recieved the latest edition of the Howard Hughes Medical Institute bulletin which contains an article about rosetta@home participants. You can download this article, and others describing other interesting work supported by the institute from

http://www.hhmi.org/bulletin/popups/download_pdfs_nov06.html


Dr. Baker,
I came across this article from HHMI bulletin and decided to join in this collaborative effort to deciphering protein structures. I just joined your team and hope that my little contribution can be of some help to your discovery. I will be graduating from college this December and pursuing a doctoral degree in biomedical sciences. Genes and proteins will certainly be my close friends. If it won\'t take too much of your time, would you describe the current protein targets in your research, as well as any recent findings? I appreciate it very much!

Sincerely,

Mike
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Message 31978 - Posted: 3 Dec 2006, 0:23:39 UTC
Last modified: 3 Dec 2006, 0:28:21 UTC

Hi Mike

Good to hear you\'re joining us!

You might not get a specific reply as the project team are pretty busy and don\'t check these message boards in full - there are mods and the rest of us that do that to help out though. There\'s info on the targets being processed in the Rosetta@home Active WorkUnit(s) Log though - that\'s probably a good starting point.

As for recent findings, some of the team went to the CASP7 confrence last week and they\'ll be reporting the findings in the coming week hopefully. The CASP7 results are here with the R@H submissions shown by the black line (they\'re entered under the team name \'Baker\').

HTH
Danny

P.S.
If you\'re having trouble getting R@H running on your computer (I just had a look and there\'s no computers listed under your account here) then post with the specifics in the number crunching forum and we\'ll try and get it sorted.

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Message 32032 - Posted: 3 Dec 2006, 22:01:37 UTC

Thanks for your information Danny. I\'m glad to be part of the team!
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Message 32039 - Posted: 4 Dec 2006, 0:07:34 UTC

Hi Proteoscientist,

I was wondering which article discusses the Rosetta in the web link that Dr. Baker mentions in his own forum and the same page you mention in a earlier post here.

Greg
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Message 32049 - Posted: 4 Dec 2006, 3:46:19 UTC

the y axis is a measure (RMSD) of how close the model is to the true structure for the fraction of the structure indicated on the x axis (from 0 to 100%). so a perfect prediction would be a horizontal line at zero. so we would like there to be at least one black line at zero all the way accross for each target (there are five black lines in each graph, one for each of the five models submitted).


It took me forever to figure out how to read these graphs, so I thought I should share my revelation with others who might be in the same situation. Please correct me if I\'m wrong here.

The graphs should be read something like this: \"For any point on one of the lines, X percent of the residues in this prediction were less than Y angstroms from their experimentally determined positions.\"
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Message 32051 - Posted: 4 Dec 2006, 3:50:47 UTC - in response to Message 32049.  

the y axis is a measure (RMSD) of how close the model is to the true structure for the fraction of the structure indicated on the x axis (from 0 to 100%). so a perfect prediction would be a horizontal line at zero. so we would like there to be at least one black line at zero all the way accross for each target (there are five black lines in each graph, one for each of the five models submitted).


It took me forever to figure out how to read these graphs, so I thought I should share my revelation with others who might be in the same situation. Please correct me if I\'m wrong here.

The graphs should be read something like this: \"For any point on one of the lines, X percent of the residues in this prediction were less than Y angstroms from their experimentally determined positions.\"



this is correct! if somebody can expand and clarify what I just posted, I\'d be delighted to replace what I wrote with the improved version.
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Message 32054 - Posted: 4 Dec 2006, 4:12:44 UTC - in response to Message 32039.  

Hi Proteoscientist,

I was wondering which article discusses the Rosetta in the web link that Dr. Baker mentions in his own forum and the same page you mention in a earlier post here.

Greg


Hi Greg,

It\'s titled \"A Cast of Thousands\" in the \"CENTRIFUGE\" section.

http://www.hhmi.org/bulletin/popups/download_pdfs_nov06.html

Mike
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Message 32056 - Posted: 4 Dec 2006, 5:30:58 UTC
Last modified: 4 Dec 2006, 5:33:56 UTC

(my attempt to reword Dr. Baker\'s comments)

The assessor reports are not yet posted. In the mean time, you can get an overview of the predictions you all made for CASP7 by looking at this url.

Each team participanting in CASP is allowed to submit up to 5 models. You can see each of our submitted models indicated by black lines. The orange lines are the models submitted by some of the other 252 groups that participated in CASP7. Not all groups submitted predictions for all of the proteins.

The higher from the bottom the line goes (Y axis), the further away from the protein\'s experimentally determined structure your prediction is (RMSD). As the line moves from left to right, it accumulates how far off your prediction for each amino acid in the structure (shown as a percentage of all the protein\'s amino acids).

A perfect prediction would be a horizontal line at zero. The first thing to note is that we are not even close to predicting protein structures perfectly! This is why we are continuing to do methods development work as a major part of Rosetta@Home, and we think the predictions would be better if they were made today than these which we made last summer. Thanks again for contributing to our efforts.

How did Baker lab do compared to the 252 other groups participating in the CASP7 experiment? One way to look at this is to count the number of times one of the Rosetta@Home models was clearly better than the models produced by other groups. You could then browse through each of the graphs, and count the number of cases one of the black lines is clearly lower than all of the orange lines for some fraction of the structure.

My son Benjamin and I just did this quickly. Our list is the following:
targets
283
299
299D1
299D2
300
307
316D3
319
323
327
329
330
330D2
331
347D2
350
354
356
357
360
363
365
368
373(?)
380

From looking at these plots, it does not seem other groups had as many \"breakaway\" models. If you have a minute, take a look at these plots and perhaps select a different group to see what their plots look like.

Also note that when our predictions are not clearly better then the others, we\'re often very close to the best predictions. This is indicative of Rosetta\'s consistently good predictions.

This \"numerical evaluation\" is only part of the story, and the measure used in these plots only looks at the position of the backbone Calpha atoms, not at the protein sidechains which, as you know, we spent a lot of time modeling as well. I\'ll give you a report on the expert evaluation and the results for the whole protein chain including sidechains in a day or two.
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use a hosting service that understands BOINC projects: http://DeepSci.com
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Message 32059 - Posted: 4 Dec 2006, 8:46:43 UTC

Would it be possible for an overview to be written of the \'participants input\' point of view.

In other words,
Could someone compile a list of the (up to) 5 entries generated by Rosetta@Home and by which participants generated that result for each target.

If it is not already available the I guess it would need David to quickly do them.

We could then write a newsletter around this showing everyone how well we have (or have not) done and linking it from direct participant input to the overview of the achievments.


[We could then add a section on the Docking we are now doing, and the CARPI]

I think this would be a nice round up. At the moment its a bit scattered ad would take some searching and tagging to compile it all together.



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Message 32064 - Posted: 4 Dec 2006, 14:39:52 UTC

That\'s a great idea Fluffy! ...and if a complete list would be too time consuming to gather, you might achieve the same effect of personalizing the results just by picking one or two of the proteins where Rosetta had a noteworthy result and list those, (and then we\'d need someone on the project team to help explain what about the result makes it noteworthy). This might help such a newsletter to stay more concise and interesting.
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Message 32065 - Posted: 4 Dec 2006, 15:04:15 UTC

yes, a newsletter including this information would certainly bring back some more people.
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Message 32387 - Posted: 10 Dec 2006, 8:01:46 UTC

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


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