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.
ping
I posted my first WU exactly 20 months ago, and just broke the 100,000 mark TODAY!
WOO HOO!!
Next target is 500WU!
P-ding!!
BTTT
the version I had running won’t restart for me - the beta expired. I still have it running on 1 pc, but my other pc is doing nothing. I didn’t see another beta out there - what next?
Two suggestions:
1. Roll back to an earlier non-beta executable.
Download the earlier executable and replace the timed-out beta executable with that earlier one. You MIGHT need to also delete your cfg file and run the executable with the “-configonly” switch to ensure it is set up properly. [Since it’s a text file, you could as easily rename the cfg file with a txt extension so you don’t lose the information in it.]
2. Get more specific help at the FAH Forums: http://foldingforum.org/
Good luck!
OK, got it. Thanks.
I thought the beta was something special, didn’t pay much attention to what I was doing... Good to have these cores going again, just have to patch my stuff at home now.
Wish I could get my macbook started. Fastest PC I have, but we use it too much...
I am able to play games on my Pentium D while using both cores - and the games (usually) run pretty well. Don’t know if I am actually getting any folding done while playing, but they keep running and don’t seem to kill my game...
Should be getting WU sent back for this and two new systems within a few days. Got to get my numbers back up!
Thanks......Colin
I don't have two separate processors, I have a single dual-core chip, so I'm thinking that the same strategy MIGHT work with a hyper-threading CPU, also.
-- OR --
Take a jog over to the folding forums and see what folks over there have to say about it.
That looks like it. I’ll give it a try. Thank you very much......Colin
In all fairness a P4 Hyper threaded CPU is not a dual core CPU. Ir WILL run two instances of F@H but not any faster than running one F@H (according to the experts). Has to do with the chip architecture and the level 1 cache.
Use of two kernals in one P4HT is discouraged because it takes each kernal longer to complete, and slightly slows the science down.
I have done it and find that I receive a few more points off the box. Go figure.
Thanks to all for keeping this thread alive while I fly to a different city every day.
Thanks for the insight. I think I’ll leave well enough alone for now. I did get F@H installed on one more computer today.
I’m going to ask my father to install on his new PC. I wonder if the units will still count, since he’s a card-carrying member of the Arkansas Democrat Party :) .....
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.
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List of Relevant Folding Links
Why Fold - Watch This !!
Extreme Overclockers Stats for FreeRepublic
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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?
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Other Useful Stuff - Links
How much are those work units worth? And what are they?
All Projects Listed
Point Summary for Workunits
Fahmon Third Party Monitoring Software
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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 #47
Next month looks like a 3-way horse race to be the next “millionaire”.
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