- Joined
- Jul 29, 2001
- Location
- Warren, OH
Want to help the world? Look here!! Folding Team32
We are team 32 and the Folding@Home software can be found at
http://folding.stanford.edu/download.html
We are currently in competition with a few other teams. Only three are outproducing us at the moment and we could use your help to retake the lead that we once had. The article below contains information and links to information about the project to help you gain an understanding of exactly what it is that we are doing.
Originally posted by YMAN
Hello ALL fellow Overclockers.com members,
I am here today to talk to you about the Folding @ Home project. The Folding @ Home project is a software program
operated and managed by Stanford University. The Folding @ Home program simulates protein folding. Understanding Protein Folding
will get us years ahead in the research of finding cures for
diseases!!! Protein Folding is done rapidly within us, but it takes
computers LONG periods of time to reproduce these complicated
Folds. This is the reason Stanford University created a Protein
Folding program for us to use on our computers. The more
processors that are used the faster we research and find cures
for diseases! The program only uses your CPUs extra cycles so
you will not even know that it is running! So why not join the
Overclockers.com Folding team? WE NEED EVERYONE to
participate! Show your Overclockers.com spirit and find cures
for diseases.
Below is an In-Depth look at the Folding @ Home project:
PROJECT GOALS: Solving the protein folding problem
Understanding how proteins self-assemble ("protein folding") is a holy grail of modern molecular biophysics. What makes it such a great challenge is its complexity, which renders simulations of folding extremely computationally demanding and difficult to understand. (See Scientific Background for more details about what are proteins, why do they fold, why this is so difficult, and why do we care).
Our group has developed a new way to simulate protein folding ("distributed dynamics") which should remove the previous barriers to simulating protein folding. However, this method is extremely computationally demanding and we need your help (see below). We have already demonstrated that our distributed dynamics technique can fold small protein fragments and protein-like synthetic polymers. The next step is to apply these methods to larger, considerably more important and complicated proteins. Unfortunately, larger proteins fold slower and thus we need more computers to simulate their folding. While the alpha helix folds in 100 nanoseconds, proteins just a little larger fold 100x slower (10 microseconds). Thus, while 10-100 processors were enough to simulate the helix, we will need many more to simulate these larger, more interesting proteins.
To achieve a significant speedup, we need lots of processors in a given run. Also, since a single run does not tell us much, we need to simulate several runs (10 runs would be a good start) per protein. Thus, we need lots of processors. By running our client that uses the Mithral CS-SDK, you can lend us your machine for as long as you like. The client allows you to run for as little or as long as you like. Even a single day's worth of running is helpful to us.
WHAT ARE PROTEINS?
Proteins are necklaces of amino acids --- long chain molecules. Proteins are the basis of how biology gets things done. As enzymes, they are the driving force behind all of the biochemical reactions which makes biology work. As structural elements, they are the main constituent of our bones, muscles, hair, skin and blood vessels. As antibodies, they recognize invading elements and allow the immune system to get rid of the unwanted invaders. For these reasons, scientists have sequenced the human genome -- the blueprint for all of the proteins in biology -- but how can we understand what these proteins do and how they work?
RELATIONSHIP TO THE HUMAN GENOME PROJECT
Since proteins play such fundamental roles in biology, scientists have sequenced the human genome. The genome is in a sense a "blueprint" for these proteins -- the genome contains the DNA code which specifies the sequence of the amino acids beads along the protein "necklace."
WHY DO PROTEINS "FOLD"?
However, only knowing this sequence tells us little about what the protein does and how it does it. In order to carryout their function (eg as enzymes or antibodies), they must take on a particular shape, also known as a "fold." Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called "folding."
One of our project goals is to simulate protein folding in order to understand how proteins fold so quickly and reliably, and to learn how to make synthetic polymers with these properties. Movies of the results of some of these simulation results can be found here.
PROTEIN FOLDING AND DISEASE: CJD (Mad Cow), Altzheimer's, ...
What happens if proteins don't fold correctly? Diseases such as Alzheimer's disease, cystic fibrosis, CJD (Mad Cow disease), an inherited form of emphysema, and even many cancers are believed to result from protein misfolding.
When proteins misfold, then can clump together ("aggregate"). These clumps can often gather in the brain, where it is believed to cause the symptoms of Mad Cow or Alzheimer's disease.
PROTEIN FOLDING AND NANOTECHNOLOGY: Building man made machines on the nanoscale
In addition to biomedical applications, learning about how proteins fold will also teach us how to design our own protein-sized "nanomachines" to do similar tasks. Of course, before nanomachines can carry out any activity, they must also be assembled.
WHY IS PROTEIN FOLDING SO DIFFICULT TO UNDERSTAND?
It's amazing that not only do proteins self-assemble -- fold -- but they do so amazingly quickly: some as fast as a millionth of a second. While this time is very fast on a person's timescale, it's remarkably long for computers to simulate. In fact there is a 1000 fold gap between the simulation timescales (nanoseconds) and the times at which the fastest proteins fold (microseconds).
A SOLUTION: DISTRIBUTED DYNAMICS
To solve the protein folding problem, we need to break the microsecond barrier. Our group has developed a new way to simulate protein folding which can break the microsecond barrier by dividing the work between multiple processors in a new way -- with a near linear speed up in the number of processors. Thus, with 1000 processors, we can break the microsecond barrier and unlock the mystery of how proteins fold.
WHAT HAVE WE DONE SO FAR AND WHERE ARE WE GOING?
Folding@Home 1.0 has been a success. During the one year period from October 2000 to October 2001, we have folded several small, fast folding proteins, with experimental validation of our method. We are now working to further develop our method, and to apply it to more complex and interesting proteins and protein folding and misfolding questions.
HOW CAN I LEARN MORE ABOUT HOW FOLDING@HOME WORKS?
A good place to start to learn about some of our success with Folding @ Home 1.0 as well as how Folding @ Home works is with some of our recent papers. Our recent paper in Physical Review Letters describes the basis of our method as well as some mathematical justifications for how we can use tens to hundreds of thousands of PCs to speed folding simulations tens to hundreds of thousands of times. Our recent paper in The Journal of Molecular Biology discusses a little more about the specifics of our method as it applies to proteins as well as our first results --- the folding of a beta hairpin.
Still not convinced?
Well this is also a competition to see with team can fold the
most! We are currently in the top 5! This is also a competition
to find who can fold the most on the overclockers.com team!
Most importantly it is how fast we can find cures for diseases
and maybe even save lives.
Below I have compiled some usefull links on Folding @ Home:
Folding @ Home official web-site:
http://folding.stanford.edu/
To find out more information:
http://folding.stanford.edu/using.html#goals
http://folding.stanford.edu/science.html#proteins
To find out all the teams stats:
http://folding.stanford.edu/cgi-bin/searchteamstats
To find out fellow Overclockers.com members stats:
http://folding.stanford.edu/cgi-bin/teampage?q=32
(See all the Overclockers.com members already Participating)
Overclockers.com Folding @ Home Web-Site:
http://www.overclockers.ws/
I hope you have chosen to participate in the Folding @ Home
Project!
If you have any questions or comments please post them!
Or feel free to PM me or one of the other Folding @ Home Participants!
- Overclockers.com Folding @ Home Participants and Stanford University
-------------------------------------------------------
This section applies if you have chosen to participate:
Download Folding @ Home software.
http://folding.stanford.edu/download.html
Once you have downloaded the program install it,
during the installation it will ask you for some information:
First it will ask you for your, Name or E-mail
In this blank put your registered overclockers.com name
Example: My name is YMAN so I put YMAN in the space provided.
Second it will ask you for a Team Number or team.
IT IS CRITICAL THAT YOU PUT 32 IN THE SPACE PROVIDED!
If 32 is not put in the space provided, you will not be considered
an Overclockers.com member in the Folding @ Home project!!!!
After the installation the program will automatically start.
Once started if will keep folding until you shut it off or exit your
operating system! Best of all you will not know that it is running!
- Folding @ Home only uses your extra, currently wasted CPU cycles!
If you have any questions or comments please post them!
Or feel free to PM me or one of the other Folding @ Home Participants!
- Overclockers.com Folding @ Home Participants and Stanford University
We are team 32 and the Folding@Home software can be found at
http://folding.stanford.edu/download.html
We are currently in competition with a few other teams. Only three are outproducing us at the moment and we could use your help to retake the lead that we once had. The article below contains information and links to information about the project to help you gain an understanding of exactly what it is that we are doing.
Originally posted by YMAN
Hello ALL fellow Overclockers.com members,
I am here today to talk to you about the Folding @ Home project. The Folding @ Home project is a software program
operated and managed by Stanford University. The Folding @ Home program simulates protein folding. Understanding Protein Folding
will get us years ahead in the research of finding cures for
diseases!!! Protein Folding is done rapidly within us, but it takes
computers LONG periods of time to reproduce these complicated
Folds. This is the reason Stanford University created a Protein
Folding program for us to use on our computers. The more
processors that are used the faster we research and find cures
for diseases! The program only uses your CPUs extra cycles so
you will not even know that it is running! So why not join the
Overclockers.com Folding team? WE NEED EVERYONE to
participate! Show your Overclockers.com spirit and find cures
for diseases.
Below is an In-Depth look at the Folding @ Home project:
PROJECT GOALS: Solving the protein folding problem
Understanding how proteins self-assemble ("protein folding") is a holy grail of modern molecular biophysics. What makes it such a great challenge is its complexity, which renders simulations of folding extremely computationally demanding and difficult to understand. (See Scientific Background for more details about what are proteins, why do they fold, why this is so difficult, and why do we care).
Our group has developed a new way to simulate protein folding ("distributed dynamics") which should remove the previous barriers to simulating protein folding. However, this method is extremely computationally demanding and we need your help (see below). We have already demonstrated that our distributed dynamics technique can fold small protein fragments and protein-like synthetic polymers. The next step is to apply these methods to larger, considerably more important and complicated proteins. Unfortunately, larger proteins fold slower and thus we need more computers to simulate their folding. While the alpha helix folds in 100 nanoseconds, proteins just a little larger fold 100x slower (10 microseconds). Thus, while 10-100 processors were enough to simulate the helix, we will need many more to simulate these larger, more interesting proteins.
To achieve a significant speedup, we need lots of processors in a given run. Also, since a single run does not tell us much, we need to simulate several runs (10 runs would be a good start) per protein. Thus, we need lots of processors. By running our client that uses the Mithral CS-SDK, you can lend us your machine for as long as you like. The client allows you to run for as little or as long as you like. Even a single day's worth of running is helpful to us.
WHAT ARE PROTEINS?
Proteins are necklaces of amino acids --- long chain molecules. Proteins are the basis of how biology gets things done. As enzymes, they are the driving force behind all of the biochemical reactions which makes biology work. As structural elements, they are the main constituent of our bones, muscles, hair, skin and blood vessels. As antibodies, they recognize invading elements and allow the immune system to get rid of the unwanted invaders. For these reasons, scientists have sequenced the human genome -- the blueprint for all of the proteins in biology -- but how can we understand what these proteins do and how they work?
RELATIONSHIP TO THE HUMAN GENOME PROJECT
Since proteins play such fundamental roles in biology, scientists have sequenced the human genome. The genome is in a sense a "blueprint" for these proteins -- the genome contains the DNA code which specifies the sequence of the amino acids beads along the protein "necklace."
WHY DO PROTEINS "FOLD"?
However, only knowing this sequence tells us little about what the protein does and how it does it. In order to carryout their function (eg as enzymes or antibodies), they must take on a particular shape, also known as a "fold." Thus, proteins are truly amazing machines: before they do their work, they assemble themselves! This self-assembly is called "folding."
One of our project goals is to simulate protein folding in order to understand how proteins fold so quickly and reliably, and to learn how to make synthetic polymers with these properties. Movies of the results of some of these simulation results can be found here.
PROTEIN FOLDING AND DISEASE: CJD (Mad Cow), Altzheimer's, ...
What happens if proteins don't fold correctly? Diseases such as Alzheimer's disease, cystic fibrosis, CJD (Mad Cow disease), an inherited form of emphysema, and even many cancers are believed to result from protein misfolding.
When proteins misfold, then can clump together ("aggregate"). These clumps can often gather in the brain, where it is believed to cause the symptoms of Mad Cow or Alzheimer's disease.
PROTEIN FOLDING AND NANOTECHNOLOGY: Building man made machines on the nanoscale
In addition to biomedical applications, learning about how proteins fold will also teach us how to design our own protein-sized "nanomachines" to do similar tasks. Of course, before nanomachines can carry out any activity, they must also be assembled.
WHY IS PROTEIN FOLDING SO DIFFICULT TO UNDERSTAND?
It's amazing that not only do proteins self-assemble -- fold -- but they do so amazingly quickly: some as fast as a millionth of a second. While this time is very fast on a person's timescale, it's remarkably long for computers to simulate. In fact there is a 1000 fold gap between the simulation timescales (nanoseconds) and the times at which the fastest proteins fold (microseconds).
A SOLUTION: DISTRIBUTED DYNAMICS
To solve the protein folding problem, we need to break the microsecond barrier. Our group has developed a new way to simulate protein folding which can break the microsecond barrier by dividing the work between multiple processors in a new way -- with a near linear speed up in the number of processors. Thus, with 1000 processors, we can break the microsecond barrier and unlock the mystery of how proteins fold.
WHAT HAVE WE DONE SO FAR AND WHERE ARE WE GOING?
Folding@Home 1.0 has been a success. During the one year period from October 2000 to October 2001, we have folded several small, fast folding proteins, with experimental validation of our method. We are now working to further develop our method, and to apply it to more complex and interesting proteins and protein folding and misfolding questions.
HOW CAN I LEARN MORE ABOUT HOW FOLDING@HOME WORKS?
A good place to start to learn about some of our success with Folding @ Home 1.0 as well as how Folding @ Home works is with some of our recent papers. Our recent paper in Physical Review Letters describes the basis of our method as well as some mathematical justifications for how we can use tens to hundreds of thousands of PCs to speed folding simulations tens to hundreds of thousands of times. Our recent paper in The Journal of Molecular Biology discusses a little more about the specifics of our method as it applies to proteins as well as our first results --- the folding of a beta hairpin.
Still not convinced?
Well this is also a competition to see with team can fold the
most! We are currently in the top 5! This is also a competition
to find who can fold the most on the overclockers.com team!
Most importantly it is how fast we can find cures for diseases
and maybe even save lives.
Below I have compiled some usefull links on Folding @ Home:
Folding @ Home official web-site:
http://folding.stanford.edu/
To find out more information:
http://folding.stanford.edu/using.html#goals
http://folding.stanford.edu/science.html#proteins
To find out all the teams stats:
http://folding.stanford.edu/cgi-bin/searchteamstats
To find out fellow Overclockers.com members stats:
http://folding.stanford.edu/cgi-bin/teampage?q=32
(See all the Overclockers.com members already Participating)
Overclockers.com Folding @ Home Web-Site:
http://www.overclockers.ws/
I hope you have chosen to participate in the Folding @ Home
Project!
If you have any questions or comments please post them!
Or feel free to PM me or one of the other Folding @ Home Participants!
- Overclockers.com Folding @ Home Participants and Stanford University
-------------------------------------------------------
This section applies if you have chosen to participate:
Download Folding @ Home software.
http://folding.stanford.edu/download.html
Once you have downloaded the program install it,
during the installation it will ask you for some information:
First it will ask you for your, Name or E-mail
In this blank put your registered overclockers.com name
Example: My name is YMAN so I put YMAN in the space provided.
Second it will ask you for a Team Number or team.
IT IS CRITICAL THAT YOU PUT 32 IN THE SPACE PROVIDED!
If 32 is not put in the space provided, you will not be considered
an Overclockers.com member in the Folding @ Home project!!!!
After the installation the program will automatically start.
Once started if will keep folding until you shut it off or exit your
operating system! Best of all you will not know that it is running!
- Folding @ Home only uses your extra, currently wasted CPU cycles!
If you have any questions or comments please post them!
Or feel free to PM me or one of the other Folding @ Home Participants!
- Overclockers.com Folding @ Home Participants and Stanford University
Last edited:
If you have any questions just ask in the F@H section of these forums.
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