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Topic: The best DC project again. (Read 6303 times) Print
phicks

Teddie
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lol  Again

Just wondering which one you folks thought had the best chance of some actual results.  I've been at this 3 yrs and can't think of anyone I've helped.  Sad  Have tried at least 6 projects of late and nothing that excites me.  I still miss FAD and wish it would resurface.   Confused  Was the only one that ever kept that fire going.  Guess I'm like many other FAD peeps and just to the point of turning everything off.  There just is no replacement.  Only thing that seems like it might actual help anyone & is exciting to me is the climate predicator stuff.  Always ran cancer related stuff is odd without them.   Thinking
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rwillis

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Quando Omni Flunkus Moritati

I like WCG, and folding for dfferent reasons. Any work that goes on with protine folding could help anyone of another projects...... most of the results are published at some piont in time, and who knows.. another reasearcher may see something that  ' lights a bulb on something else' that IMHO is the most important reason to keep crunching. That has been the driving force behind so many discoveries, one researcher is work on a totally different problem, and stumbles on an approach for another....... again just my opinion.... but that is waht keep me going.


Rick
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PiNkY

the dang enigma
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*squeek*

Quote from: "phicks"
best chance of some actual results.

not sure what the climate predictor(s) (is the newish one i've heard about supposed to be the same as the old one?) are actually doing, but...


wcg's hpf seems dependent on someone actually doing something with what they come up with - they're making a database of the stuff they come up with, to my understanding. *shrug*  if noone makes use of the database, things seem to end up like fad... Huh  does seem an ok project if things do work out, though.

haven't looked much into wcg's [email protected] thing...

grid left out intentionally as i'm sure my opinion on it is known Tongue

[email protected] seems to be focused on improving on the rosetta application....not sure if anyone other then wcg/grid is using the rosetta app, but it seems to follow the same line of thought with earlier mentioned wcg hpf.

folding at times seems kinda vague at times, but i like seeing that they are actually using what they're getting, and publishing it...

Quote from: "from [url=http://folding.stanford.edu/FAQ-diseases.html
here[/url]"]To date, FAH has been very successful, with over 25 published works in the first five years directly stemming from FAH calculations (and lots more on the way). We will continue to work on all fronts: new scientific cores, new server side algorithms, new models for proteins, and new questions related to testing our methods and applications to disease and other biomedical questions.


actually seeing something being done with the data is enough to keep me involved i guess.


i don't know much about a lot of the smaller projects, so i'll leave that to others...
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Scribe

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Scribbling to Order

If you want a project that is 'going somewhere' then Rosetta certainly keeps you well informed....unlike some....
Quote
January 25, 2006

I will use this space to give biweekly updates on recent results and the work units planned for upcoming weeks.

Today I will begin by summarizing some of the main results of the last few weeks.

More computing power can significantly improve results. This is illustrated by the 1ogw case. For one of the work unit types (NO_SIM_ANNEAL_BARCODE_30) we ran 60,000 independent jobs, for a total of 600,000 structures. If we take the lowest energy ten structures, the median rmsd is 2.86. If we instead take the lowest energy ten structures just from the first 18,000 jobs, the median rmsd is 4.49. So with more sampling, we are able to land more explorers closer to the global minimum, and get more accurate results.
Allowing additional flexibility in the chain can significantly improve results (this was the "breakthrough" I described several months ago). In the "NO_VARY_OMEGA" runs, we went back to the pre breakthrough less flexible chain, and the results were consistently worse. For example, in the 1ogw case, the median rmsd of the low energy structures increased to 4.50. For 1r69, the median rmsd of the low energy structures increased from 1.29 to 2.80.
The computationally less expensive NO_SIM_ANNEAL methods were no worse in locating low energy low rmsd structures than the SIM_ANNEAL runs. This is good news, as we can carry out many more of the NO_SIM_ANNEAL searches and so do more searching for the same amount of CPU time.
As Paul Buck anticipated, most of the remaining alternative methods we tested were roughly equivalent (except for the NO_VARY_OMEGA). One way of looking at this is that given the huge space we have to search, all that matters is how many independent explorers are sent out to search, not the details of the instructions each are given about where to search.
Excitingly, for many of the proteins, the lowest energy structures are very close (less than 3.0A rmsd) from the true structure. For example, in the NO_SIM_ANNEAL_BARCODE_30 the rmsds of the lowest energy structures are
1dtj: 1.93
1dcj: 2.72
1ogw: 2.65
2reb: 1.46
1r69: 1.79
1di2: 1.40

These results are a significant improvement over anything that has been done before. If we are able to do this consistently for proteins in this size range, it will be a major scientific breakthrough.

Our next step will be to test out the computationally efficient NO_SIM_ANNEAL_BARCODE_30 method on 25 new proteins we haven't done calculations on yet. You will see the new proteins on your screen saver by early next week. The "BARCODE_30" means that for every 30 amino acid residue segment in the protein, a random choice as to the value of the angles for one residue are randomly picked at the beginning of the run. This directs different runs to explore different regions of the space, and is more or less equivalent to directing different explorers to different lattitudes and longitudes.

You will also see more "PRODUCTION_AB_INITIO" runs in the next few weeks. In these runs we are testing the first low resolution part of the search. We will lower the number of trajectories per work unit to avoid the max_cpu_time problem. I think we have largely solved this problem now by going to shorter work units and doubling the max_cpu_time limit.

There will also be tests of calculations for some of the other projects described in the introduction section of the web site. We hope to get the vaccine design calculations running on BOINC in the near future. With regard to the message board posts, we aren't yet doing any work on diabetes or MS specifically, but if we can generate accurate structures of proteins involved in these diseases using the methods you are helping us to develop, it will contribute to efforts to develop therapies.

Thank you again for all of your wonderful contributions!

David Baker


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Teletraan

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I definitely prefer the Human Proteome project (run through WCG, of course,  NOT grid!  MrGreen ).

Besides having an interest in the subject matter, I prefer the project based on the Rosetta application itself. In the CASP experiments (Critical Assessment of Techniques for Protein Structure Prediction) Rosetta was shown to be far superior for protein prediction than any of the other competing models.
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phicks

Teddie
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Ok you WCG folks why do you prefer that one over [email protected]?  Thinking
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Teletraan

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[email protected] is focused on revising the actual Rosetta program to be able to better predict protein structures. It doesn't actually crunch any data that will be added to the proteome database for researchers to use, as far as I know.

WCG uses the current version of Rosetta to actually produce data for scientists to use. So I prefer to crunch at WCG.
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tebrino

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Bad boi

If all cancer/proteome research programs work like Grid, than [email protected] is most likely to produce any results MrGreen
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Join SeriousCrunchers team @ WCG - You know it is your destiny!

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Teletraan

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lol
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phicks

Teddie
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Hehe  lol
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Mr. Snrub

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Here is a good explanation and comparison of many DC projects:

http://www.hyper.net/dc-howto.html
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phicks

Teddie
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Very good reading.  Cheesy
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pwrguru

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I agree.... It was very long but very good reading......
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Matt3223

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I'm with Scribe above>........

I've been on the grand tour of DC projects myself lately.............I "like" alot of them!....fav's are probable Einstein just for the science interest.  As far as actual usable results I'd have to put [email protected] and Rosetta at the top.  WCG is looking pretty good.


At the moment though.......as far as perceived usefullness and direct interest for us crunchers I'd have to say that I've been convinced that [email protected] is now the top dog.

David Baker the project leader is very involved..........the project does more direct things than just "develop" the software........in that the development has pretty advanced ramificatioins for disease.

Read about some of these new developments.........there is currently a world wide CASP7 contest they are participating in...

Quote from: David Baker
We will have to have prizes when CASP finishes at the end of July for the top overall team and the
top team during CASP. definitely a citation in the science paper on rosetta distributed contributing at the minimum!

............

We will be keeping track of the total credits earned by each team from the period May 10 to Aug 1 when CASP ends, and will describe the winning teams and their contributions to the CASP prediction efforts in the above article and in book chapters on distributed computing we will be writing at the end of the summer.

from here:  http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177

HOW ABOUT THAT!  Can't beat an actual citatioin in a research paper result from crunch work!

and the project has been awarded a piece of the $287 million award for funding that the Gates foundation has awarded for advanced HIV vaccine research...........Rosetta is investigating hopes from "designing" custom proteins to trigger an antibody response...

See here:  http://seattlepi.nwsource.com/local/278100_aidsvaccine19ww.html

it's very exciting once you dig down a little deeper into what they are doing........

see here also:  [email protected] Disease Related Research

excerpt: 
Quote
rest assured that the structure prediction calculations currently running on your computers will have direct bearing on treating disease. There is a three-fold explanation for this direct relationship between structure prediction and disease treatment:

   1. Structure prediction and protein design are closely related.

            Improvements in structure prediction lead to improvements in protein design, which in turn can be directly translated into making new enzymes, vaccines, etc. For more information on protein design you might be interested in looking at the review we recently wrote in science which is available at our home page (http://depts.washington.edu/bakerpg).

            Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., Baker, D. (2005). Progress in modeling of protein structures and interactions Science 310, 638-642.

   2. Structure prediction identifies targets for new drugs.

            When we predict structures for proteins in the human genome on a large scale, we learn about the functions of many proteins, which will help in understanding how cells work and how disease occurs. More directly, we will be able to identify many new potential drug targets for which small molecule inhibitors (drugs) can be designed. To put this in context, one major road-block to developing new treatments for human disease is identifying new "drugable" protein targets. Most new drugs these days interact with the same targets as the old drugs, so these drugs lead to only small improvements in disease treatment. Structure prediction helps us identify new drug targets, and so will help us find innovative, perhaps even breakthrough, treatments for disease.

   3. Structure prediction allows us to use "rational design" to create new drugs.

            If we know the structure of a protein, we can determine its functional sites, and specifically target those sites to be inactivated by a new drug. Calculation of whether a small molecule (drug) will bind to and inactivate a protein target is similar in many ways to the structure prediction calculations we are doing here--it is basically a problem of finding the lowest energy structure of the protein plus drug system--and we have recently developed a new module in ROSETTA to do this docking problem. Results are very promising, and in the near future your machines will likely be running drug docking calculations along with the vaccine and therapeutic protein design projects described above, in addition to the protein folding calculations you are doing now.


There are lots of good projects............but [email protected] and Rosetta seem to release the most scientific papers and active disease research with forseable results...........

I'd say give Rosetta a closer look!  My Rosetta credits will be on the RISE!!!!!!!

David Baker even keeps a running journal on the forums for everyone.........VERY NICE!!!

http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177

that's my two cents for today at least!!!!!!!!
Last Edit: July 21, 2006, 10:00:54 PM by Matt3223
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