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Folding@Home - Binding of a Ligand (small molecule drug) to Proteins
Stanford University Biotechnology Dept ^ | Jan 03, 2008 | Peter Kasson

Posted on 01/03/2008 9:17:05 PM PST by texas booster

We're often interested in comparing things--predicting a known difference is a good way to test our methods. Then, once we're pretty confident that things work, we want to predict ways to change the way proteins interact. Changing a system in a defined way is both a good tool for biological insight and the basis for a lot of medical treatments.

In this particular case, we're interested in the "selectivity" of ligand binding by a protein: the protein is known to bind one small molecule ("ligand") much better than another. So project 3903/3905 is a pair of projects comparing the protein-small molecule interactions, one project for each small molecule. Project 3906/3907 are the essential "control" projects that tells us how different the small molecules are in the way that they interact with the water around them. When we combine these pairs of projects, we can then calculate the difference between the "bound" state in which the protein is interacting with the small molecule and the "unbound" state in which the protein and small molecule each just interact with the environment. There are experimental data on the difference between these two small molecules; if we get good results here, we'll go on to test a number of interactions that aren't experimentally known yet.

The trick is that some protein-small molecule interactions are quite easy to test experimentally and some are very hard. Using Folding@Home, they are all moderate in difficulty. So if we can validate our methods on the "easy" ones, we can then predict the "hard" ones. Usually only a small fraction of protein-small molecule interactions that one tests turn out to be important. For the ones we predict are really interesting, we can do the experiment. But Folding@Home allows us to skip the experiments that are both hard and likely not to be interesting. This sounds simple, but it can be very powerful in trying to understand the underlying biology.

We also hope that it can help us understand a number of diseases and drug interactions better. For instance, a number of diseases or "failures" of medical therapy are due to mutations in proteins (changes to their amino acid sequence). We would like to understand how these mutations affect the interactions between the protein and the drug. If we can understand that, we can help suggest ways to improve the drug therapy. This is obviously a large, hard problem, but we think that Folding@Home can play an important role here.


TOPICS: Health/Medicine
KEYWORDS: alzheimers; fh; foldinghome; protein
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We often wonder what we are folding, and the pretty pictures of molecules don't really tell us much.

Dr. Kasson discusses the art of computer modeling as it relates to proteins and drug interaction.

Please consider joining the Free Republic folding team #36120 to use your idle computer time helping to advance medical research.

Remember the research that you contribute today may result in the cure that extends your life tomorrow!

1 posted on 01/03/2008 9:17:06 PM PST by texas booster
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To: Leofl; leow; LFOD777; LibWhacker; Live free or die; LogicBomb; LonePalm; Lost Dutchman; LRS; ...
What better time to join the Free Republic Folding@home effort than a FReepathon during the Presidential election season!

Please consider donating to keep Free Republic running strong!

After donating, follow this thread and install the F@H kernal, or just check your systems to ensure that they are all folding for you and team 36120!

BTW, the update for ATI graphics cards should be out within a month.

2 posted on 01/03/2008 9:21:25 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
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To: 1066AD; 11Bush; A.Hun; abner; AbsoluteGrace; Advil; aft_lizard; agooga; ahayes; aliquando; ...

What better time to join the Free Republic Folding@home effort than a FReepathon during the Presidential election season!

Please consider donating to keep Free Republic running strong!

After donating, follow this thread and install the F@H kernal, or just check your systems to ensure that they are all folding for you and team 36120!

BTW, the update for ATI graphics cards should be out within a month.


3 posted on 01/03/2008 9:22:37 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
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To: texas booster
Folding@Home FAQ for new users:

What is Folding@Home?
A Stanford University project to find out how proteins fold.

Why it's important: Proteins folding wrong causes all kinds of diseases, like Alzheimer's, Parkinson's, and forms of cancer. Folding@Home uses novel computational methods and large scale distributed computing, to simulate timescales thousands to millions of times longer than previously achieved. Through Folding@home, scientists now have the horsepower to study the mechanics of protein folding. With its ability to share the workload among hundred of thousands of computers economically, Folding@home can help scientists understand how proteins snap, or don't, into their predestined shapes - and may help to explain the origins of diseases such as Alzheimer's and apparently unrelated diseases. We're fueling research that could end all that.


How does it work?: You download a safe, tested program (see link below) that is certified by Stanford University. It gets work from Stanford, runs calculations using your spare computer power, and sends the results back to the University.

Is it safe? Yes! Folding@Home rarely effects computer performance in any way and won't compromise your privacy in any way. It only uses the computing power you aren't using so it doesn't slow down other programs.


How do I get started folding for Team FreeRepublic?:
1.) Download the folding program from Stanford University's folding download page (Folding@home Client Download). Type in your desired user-name.
2.) Type in 36120 for the team number. THIS IS VERY IMPORTANT - if you get the number wrong, you won't be folding for team FreeRepublic!
3.) The third question asks, "Launch automatically at machine startup, installing this as a service?" - We recommend you answer YES. Otherwise you will have to manually start the program after every reboot.


How can my computer help? Even if they were given exclusive access to all of the world's supercomputers, Stanford still wouldn't have as much processing power as they get from the supercluster of people's desktop systems Folding@home relies on. Modern supercomputers are essentially a cluster of hundreds of processors linked by fast networking. But Stanford needed the power of hundreds of thousands of processors, not just hundreds.


There's no reason to not get involved! It's free, easy, and you can know you're helping every minute without lifting a finger.

*******************************************

List of Relevant Folding Links
Why Fold - Watch This !!


Another Folding Clip


The Inner Life of a Cell


Folding@home Client Download


FreeRepublic.com Folder Stats


Extreme Overclockers Stats for FreeRepublic


Another Stats Page


*******************************************
Competition (Not!!) Dummies ..Daily Kos


Dummie Folding Threads #7 #8 #9#10#11 #12
Hey DUmmies, can't ya'll post a new thread at least once a year?


**************************************************
Other Useful Stuff - Links


How much are those work units worth? And what are they?
All Projects Listed
Point Summary for Workunits


Stat Image Generator


Fahmon Third Party Monitoring Software

**************************************
Past FreeRepublic Folding threads


#1 #2 #3 #4 #5 #6 #7 #8 #9 #10 #11 #12 #13 #14 #15 #16 #17 #18 #19 #20 #21 #22 #23 #24 #25 #26 #27 #28 #29 #30 #31 #32 #33 #34 #35 #36 #37 #38 #39 #40 #41 #42 #43 #44 #45 #46

4 posted on 01/03/2008 9:24:50 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
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To: uglybiker; All
For those that are interested, there is a FReeper team for SETI@Home. SETI has been in the news lately, and I know that many of us have worked the project in the past.

Here is a thread discussing an update to Arecibo and the new data streaming from the radio telescope.

And please reserve at least one system for F@H!

5 posted on 01/03/2008 9:28:07 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
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To: texas booster

I just joined and I’m already up to 384, hehe


6 posted on 01/03/2008 9:39:25 PM PST by Oshkalaboomboom
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To: texas booster

I stopped running it because it won’t let the screen saver activate, tho’ it used to.


7 posted on 01/03/2008 10:10:17 PM PST by 1066AD
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To: texas booster
Is there a console program for Duel cores that will use both cores? The one I tried didn’t like my ati graphics card. The first 2 WUs never upload when done. The next two did upload.
8 posted on 01/03/2008 10:11:23 PM PST by ThomasThomas (Thomaswithah)
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To: Oshkalaboomboom

Congrats! Just check the stats page every so often and make sure that your systems are still finishing work units, and that you are getting credit for them.


9 posted on 01/03/2008 10:17:51 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
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To: 1066AD
If you were running the GUI version (that’s the one with the little red flower in the bottom corner), there should not be much of a conflict between the two.

I always turned off my screensaver so that F@H would get more computer cycles to complete the work.

Since the screensaver is important to you, download the console version 5.04 of F@H here:

http://folding.stanford.edu/English/Download

Save it to your F@H directory, and the run the program. You enter the normal stuff (Name, Team #36120), enter no to proxy but YES to Advanced Options.

Inside advanced options enter 75% (your choice) on CPU time, default down to “Always use advanced scientific...” and call this one Machine ID 2. It doesn’t hurt to call it 1, but just to keep thinks clear.

Let it run for about 10 minutes while connected to the Internet, then close the DOS box and restart the system.

You should never have a conflict between the two programs again.

10 posted on 01/03/2008 10:26:06 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
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To: ThomasThomas
Ok a couple of questions here.

Exactly which ATI cards are you using, and how much memory on the cards?

If you have a dual core system and over 1 GB of RAM you could try the SMP program. I got tired of fighting Vista to keep it running so I now load two folders of F@H on my dual core systems, F@H1 and F@H2.

Copy the F@H console 6.01 beta into each folder, then run each one.

You will get a DOS box where you can put in thomasthomas, team 36120, no to proxy and IE, but yes to Advanced Options.

Hit enter to accept the default choices until you get to “Use advanced scientific ...” and select Yes.

Make sure that you chose No for deadlineless core. They are not used at this time.

When you come to the section that says machine ID 1: select “1 for F@H1. Let it download and run for about 10 minutes.

Go to folder F@H2 and repeat the process, except this time enter “2” at Machine ID. Let this box run for about 10 minutes.

Close both DOS boxes and restart the system. They will be running in the background and F@H will assign the work to each core, from each F@H folder.

Please let me know how it goes!

11 posted on 01/03/2008 10:35:31 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
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To: texas booster
Thanks for keeping us up to date on the Team 36120, texas booster. Here's some info for those looking for what kind of assistance they can get from the community supporting Stanford and Folding@home:

Folding@home Support Forum

[Will open in new window so you don't
lose your place here at Free Republic]

          The board is run under phpBB ver.3, and has several very knowledgeable Moderators that can assist in all aspects of the programming, and resolving any issues you may run into on your system. They also have contacts with and into the Stanford Labs and Dr. Pande's team if necessary.
          Here is a list of the headers currently active:

Board Headings:

          I'm a dunce when it comes to what's beneath the covers of my PC, but with the help from the folks here on FR and the crew at F@H have managed to get my WinME and WinXP both running consistently with few problems, and they are helping the science develop new breakthroughs.
          So send your money to FR, and your points to F@H -- both are necessary for a free society.



12 posted on 01/03/2008 10:59:19 PM PST by brityank (The more I learn about the Constitution, the more I realise this Government is UNconstitutional !!)
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To: brityank

Thanks for the links. I need to put the Support Forum back into my Bookmarks.


13 posted on 01/03/2008 11:05:49 PM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
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To: texas booster

The link is available from F@H’s main page, on the left side. The old forum got clobbered last November, so they are rebuilding it on this one. Most of the info from the old one is available through the Mods on the new board, but we can’t get to it. Saved my butt (folding-wise) a couple of times.


14 posted on 01/03/2008 11:19:00 PM PST by brityank (The more I learn about the Constitution, the more I realise this Government is UNconstitutional !!)
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To: texas booster

BTTT


15 posted on 01/04/2008 2:55:44 AM PST by E.G.C.
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To: texas booster

Laundry bump


16 posted on 01/04/2008 3:20:42 AM PST by dfwddr (Duncan Hunter '08 -- the real thing.)
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To: texas booster

I will have to give this a shot...thanks.


17 posted on 01/04/2008 5:15:46 AM PST by LearnsFromMistakes (Member VRWC - Volvo-owning right-wing conspiracy.)
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To: All
My shameless self-promotion for this thread:

If you're interested in tracking your folding machine(s) over the web, please Freepmail me or follow the links below.

Available features include:

Links

Please Freepmail me with any questions.

18 posted on 01/04/2008 5:26:50 AM PST by Egon ("If all your friends were named Cliff, would you jump off them??" - Hugh Neutron)
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To: E.G.C.

Thanks for your consistent bumps in the night.

Hope that Christmas and the New Year have been GREAT for you!


19 posted on 01/04/2008 5:40:32 AM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
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To: LearnsFromMistakes

Please ping is you have any questions.

I’ll keep an eye out for your first points here:

http://folding.extremeoverclocking.com/user_list.php?s=&a=2&t=36120


20 posted on 01/04/2008 5:42:03 AM PST by texas booster (Join FreeRepublic's Folding@Home team (Team # 36120) Cure Alzheimer's!)
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