DISCUSSION of Rosetta@home Journal (2)

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casio7131

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Message 27642 - Posted: 20 Sep 2006, 3:31:09 UTC

i don't think that the mods are causing the problems; rather, it's people (from both sides) continually dredging over old issues trying to score cheap points amongst themselves. i wish they'd all just give up on it!
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Jose

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Message 28061 - Posted: 21 Sep 2006, 18:35:58 UTC

Sorry David: one of the moderators you introduced is the worst flamer and trouble maker that post in the MBs.

And the other three have been rather inefficient .
This and no other is the root from which a Tyrant springs; when he first appears he is a protector.”
Plato
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R.L. Casey

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Message 28100 - Posted: 21 Sep 2006, 19:23:18 UTC

It's exciting to see the 'PSH......' Work Units coming. An interesting early effect has been seen in that at least some of these Work Units generate a substantially larger number of decoys per unit CPU time than other recent WUs such as the CASP refinements, LARS runs, or 'FARELAX...' cases. Is there something about the structure of these 'PSH' proteins that induces that effect?
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Possu
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Message 28130 - Posted: 21 Sep 2006, 22:34:48 UTC - in response to Message 28100.  

They are easier problems. Because the HIV protein is quite large, we are modeling it in smaller chunks, only one loop at a time (usually only 5-10 amino acids long). So if you happen to get one of those calculations, you will notice that the structure showing in the graphics window/screen saver looks like discontinuous fragments. That's the region we are refining at the moment. Bigger chunks will come later.
Also people will probably notice that the structure doesn't move much because a lot of the movements are occuring on the sidechain level and rosetta@home haven't has the ability to show sidechains yet.

Thanks for all the cpu time.

It's exciting to see the 'PSH......' Work Units coming. An interesting early effect has been seen in that at least some of these Work Units generate a substantially larger number of decoys per unit CPU time than other recent WUs such as the CASP refinements, LARS runs, or 'FARELAX...' cases. Is there something about the structure of these 'PSH' proteins that induces that effect?


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R.L. Casey

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Message 28138 - Posted: 22 Sep 2006, 1:00:09 UTC - in response to Message 28130.  

They are easier problems. Because the HIV protein is quite large, we are modeling it in smaller chunks, only one loop at a time (usually only 5-10 amino acids long). So if you happen to get one of those calculations, you will notice that the structure showing in the graphics window/screen saver looks like discontinuous fragments. That's the region we are refining at the moment. Bigger chunks will come later.
Also people will probably notice that the structure doesn't move much because a lot of the movements are occuring on the sidechain level and rosetta@home haven't has the ability to show sidechains yet.

Thanks for all the cpu time.

It's exciting to see the 'PSH......' Work Units coming. An interesting early effect has been seen in that at least some of these Work Units generate a substantially larger number of decoys per unit CPU time than other recent WUs such as the CASP refinements, LARS runs, or 'FARELAX...' cases. Is there something about the structure of these 'PSH' proteins that induces that effect?


Thank you for the opportunity to serve!
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Message 28603 - Posted: 28 Sep 2006, 5:45:00 UTC - in response to Message 28602.  

Laura has just posted a new version of her rosetta@home video--see her post in the rosetta video thread below. If you have a chance, take a look and post in her thread any suggestions you have for improving it.

where is the link????????
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Message 28604 - Posted: 28 Sep 2006, 5:50:07 UTC - in response to Message 28603.  

Laura has just posted a new version of her rosetta@home video--see her post in the rosetta video thread below. If you have a chance, take a look and post in her thread any suggestions you have for improving it.

where is the link????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282
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Message 28605 - Posted: 28 Sep 2006, 6:00:07 UTC - in response to Message 28604.  

[quote]Laura has just posted a new version of her rosetta@home video--see her post in the rosetta video thread below. If you have a chance, take a look and post in her thread any suggestions you have for improving it.

where is the link????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282[/quotecant get it to work can you sent the link so i could click on it?????????
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Message 28606 - Posted: 28 Sep 2006, 6:06:42 UTC - in response to Message 28605.  

[quote]Laura has just posted a new version of her rosetta@home video--see her post in the rosetta video thread below. If you have a chance, take a look and post in her thread any suggestions you have for improving it.

where is the link????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282[/quotecant get it to work can you sent the link so i could click on it?????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282#28570

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Message 28607 - Posted: 28 Sep 2006, 6:30:07 UTC - in response to Message 28606.  

[quote]Laura has just posted a new version of her rosetta@home video--see her post in the rosetta video thread below. If you have a chance, take a look and post in her thread any suggestions you have for improving it.

where is the link????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282[/quotecant get it to work can you sent the link so i could click on it?????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282#28570


ok thanks anyway i just cant get to the link
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Message 28613 - Posted: 28 Sep 2006, 11:17:12 UTC - in response to Message 28606.  

[quote]Laura has just posted a new version of her rosetta@home video--see her post in the rosetta video thread below. If you have a chance, take a look and post in her thread any suggestions you have for improving it.

where is the link????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282[/quotecant get it to work can you sent the link so i could click on it?????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282#28570



You should put url tags tound it to make it easier for people ;-)

The Video is here (large download)
http://www.lauralynngonzalez.com/things/rosettateam/bakerSmall.mpg
Talk from the point of this new one is
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282#28558

Anyways, it gives the mods something to clean up :-D (we're not suppose to post in DB's journal.) <oops>
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Message 28614 - Posted: 28 Sep 2006, 11:17:59 UTC - in response to Message 28606.  

[quote]Laura has just posted a new version of her rosetta@home video--see her post in the rosetta video thread below. If you have a chance, take a look and post in her thread any suggestions you have for improving it.

where is the link????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282[/quotecant get it to work can you sent the link so i could click on it?????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282#28570



You should put url tags tound it to make it easier for people ;-)

The Video is here (large download)
http://www.lauralynngonzalez.com/things/rosettateam/bakerSmall.mpg
Talk from the point of this new one is
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282#28558

Anyways, it gives the mods something to clean up :-D (we're not suppose to post in DB's journal.) <oops>
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Message 28616 - Posted: 28 Sep 2006, 11:58:10 UTC - in response to Message 28614.  

[quote]Laura has just posted a new version of her rosetta@home video--see her post in the rosetta video thread below. If you have a chance, take a look and post in her thread any suggestions you have for improving it.

where is the link????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282[/quotecant get it to work can you sent the link so i could click on it?????????


https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282#28570



You should put url tags tound it to make it easier for people ;-)

The Video is here (large download)
http://www.lauralynngonzalez.com/things/rosettateam/bakerSmall.mpg
Talk from the point of this new one is
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=1282#28558

Anyways, it gives the mods something to clean up :-D (we're not suppose to post in DB's journal.) <oops>

i saw the video . thanks. will send to everone i know
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Message 29381 - Posted: 15 Oct 2006, 11:56:27 UTC

The thing about an interactive rosetta sounds sweet :) , but how do we know that the protein we design is able to cure a desease?
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Message 29407 - Posted: 15 Oct 2006, 22:02:15 UTC - in response to Message 29381.  

The thing about an interactive rosetta sounds sweet :) , but how do we know that the protein we design is able to cure a desease?


If rosetta goes interactive, I'll probably just stop ever bothering to get up from my computer. I'm not complaining, though. All of these new features and new science are going to bring a lot of people in and keep those of us who are already here coming back for more. I'm very impressed.
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David Baker
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Message 29411 - Posted: 15 Oct 2006, 22:31:35 UTC - in response to Message 29381.  

The thing about an interactive rosetta sounds sweet :) , but how do we know that the protein we design is able to cure a desease?


good question! all of the work units we would send out would keep the part that would be important for curing the disease constant but the other parts would be variable. this is what we are doing now, your computers are exploring different possibilities for the variable regions. if we can go interactive, you would help your computer explore the different possiblities. we would rank all the solutions that each of you return by their energies, and then experimentally test the lowest energy solutions.
now, suppose that you designed a protein and it turned into a blockbuster drug--maybe you should get some fraction of the royalties? thus far all income from licensing rosetta to companies has gone straight back into research and development and I want this to continue, but the double incentive of contributing both to global health and possibly getting some money back could make this vision of an interactive multiplayer rosetta "game" quite popular globally which would be great for human health and research (and who knows, there could be a 13 year old in Nepal who turns out to be a whiz at designing proteins!). but I should emphasize that this is still more fantasy than reality right now.


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Message 29413 - Posted: 15 Oct 2006, 23:49:22 UTC

Just read your mention about a possible interactive mode in which participants could try for themselves to find the best way to fold the protein with all its knotty branches. This caused me to remember hearing that some artists have to make chandeliers by interlocking antlers together, and that it is a difficult task, a test of their ability.
Would some such people, (or others who work with interlocking puzzles), be worth tapping into for efforts in your new upcoming interactive mode?
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Message 30449 - Posted: 1 Nov 2006, 15:38:40 UTC

RE: user-directed / interactive Rosetta. You mention putting the current 5 or 10 best models into the download so you can work them from that point. Don't forget to put the native structure into such an alterable position as well, when it is known.

Why? Because, if it's like a Rubic's cube. Starting with the perfect answer, and disturbing that, and then learning how to put it back is good training for the real thing. Learning how to play the end-game may be prelude to learning how to make moves when further from the end-game. So if we twist and turn the native structure and learn how it behaves when it is CLOSE to correct, we can see what it is that makes the energy levels INCREASE, and therefore learn the types of things that make them decrease at the same time.
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 30461 - Posted: 1 Nov 2006, 18:23:17 UTC

Interactive Rosetta - good Idea! In this wu:

"FRA_t364_HOMOENV_hom001_6_t364_4_1s5uA_IGNORE_THE_REST_545_1324_8_0"

On the graphic display the red colored end is pointing from the main structure into the middle of nothere, but it may fit perfect into the blue colored section by wrapping the red end around the blue section. The algorithm does not find this solution. May be there is a high potential barrier between the starting point and this possible solution.

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Message 30484 - Posted: 2 Nov 2006, 3:49:05 UTC

Regarding the upcoming interactive mode: How does the protein "sense" its own energy level, if it indeed does so? Could the interactive mode provide "feedback" about what the energy level is at each point of the manipulation so that the neophyte protein-artist could have an immediate sense of the usefulness of a particular move, in seeking the lowest level?
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