Is folding worth it, and does it make a difference? - Overclock.net

Knitelife · 07-14-07

Is folding worth it, and does it make a difference?

There has been many threads where questions like this have been asked. To be honest, they used to bother me. Questions like:

Is it worth it?
Does it actually help?
What if it does not actually find a cure?
Why should I fold?
Do you fold for science or points?

As I thought about these questions, I realized they are actually all good questions. Answering these questions are not as simple. The root of many of these questions is based on a misunderstanding of what folding actually is and how it is used.

I won’t go into the technical part of folding, as that would require a whole separate thread. But I will attempt to shed so light why I fold. Hopefully with the help of some greater minds than mine, you will find some answers to the questions above for yourself.

When I see the questions “What if it does not actually find a cure”, I am reminded of the old Batman series. Rememeber the Bat Cave, with the big computer boxes with big multi color buttons. Batman and Robin would feed all the information they had into the system, and the computers lights and buttons would all flash. In the end a little card would pop out with an answer to whatever they were looking for.

Folding is not the answer, it is a means to understand the problem, and hopefully find the answer.

Quote:

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 make 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?

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, it takes about a day to simulate a nanosecond (1/1,000,000,000 of a second). Unfortunately, proteins fold on the tens of microsecond timescale (10,000 nanoseconds). Thus, it would take 10,000 CPU days to simulate folding -- i.e. it would take 30 CPU years! That's a long time to wait for one result!

A SOLUTION: DISTRIBUTED DYNAMICS
To solve the protein folding problem, we need to break the microsecond barrier. Our group has developed multiple new ways 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 power of Folding@Home (over 100,000 processors), we have successfully smashed the microsecond barrier, simulating milliseconds of folding time and helped to unlock the mystery of how proteins fold.

Source: http://folding.stanford.edu/science.html

So folding is basically utilizing the power of thousands of computers to simulate how proteins fold. The key word here is simulate. Scientists can test many different proteins, as well has how they are affected by their environment. This helps them better understand how a protein folds and what forces affect the outcome of protein folding.

Quote:

Equipped with his five senses, man explores the universe around him and calls the adventure Science. ~Edwin Powell Hubble, The Nature of Science, 1954

Nature composes some of her loveliest poems for the microscope and the telescope. ~Theodore Roszak, Where the Wasteland Ends, 1972

The results produced by the folding project can then be analysed. With any luck, scientists and researchers can identify patterns, odd occurrances, and unknown behaviors. They can also test their expectations against actual results. This allows them to learn and adjust their understanding of how protein folding works.

Quote:

The most exciting phrase to hear in science, the one that heralds the most discoveries, is not "Eureka!" (I found it!) but "That's funny..." ~Isaac Asimov

The important thing in science is not so much to obtain new facts as to discover new ways of thinking about them. ~William Lawrence Bragg

With advances in technology, for the first time in human history, things like this can actually be attempted. It was not long ago that even considering something as ambitious as what Stanford is trying to do would be unthinkable.

Quote:

A science is any discipline in which the fool of this generation can go beyond the point reached by the genius of the last generation. ~Max Gluckman, Politics, Law and Ritual, 1965

Great scientific discoveries have been made by men seeking to verify quite erroneous theories about the nature of things. ~Aldous Huxley

What if folding does not produce a cure?
In the end, folding will not produce the cure, it has and will continue to produce results for researchers to study. These results teach us things we did not know, or had not considered. The more we learn, the more we adapt our understanding of nature and its mysteries. Folding will never replace the human mind. And with the right tools, time, and curiosity, the human mind will find the cure.

Quote:

Research is the process of going up alleys to see if they are blind. ~Marston Bates

The scientist is not a person who gives the right answers, he's one who asks the right questions. ~Claude Lévi-Strauss, Le Cru et le cuit, 1964

Scientific principles and laws do not lie on the surface of nature. They are hidden, and must be wrested from nature by an active and elaborate technique of inquiry. ~John Dewey, Reconstruction in Philosophy, 1920

An experiment is a question which science poses to Nature, and a measurement is the recording of Nature's answer. ~Max Planck, Scientific Autobiography and Other Papers, 1949

Discovery is seeing what everybody else has seen, and thinking what nobody else has thought. ~Albert Szent-Gyorgi

So am I actually making a difference? Why should I fold?
No matter how large or small your contribution, you do make a difference. The concept behind folding is teamwork. When enough people help a little, a lot gets done.

Quote:

Give me a lever long enough and a fulcrum on which to place it, and I shall move the world. ~ARCHIMEDES

It is the tension between creativity and skepticism that has produced the stunning and unexpected findings of science. ~CARL SAGAN

There is a single light of science, and to brighten it anywhere is to brighten it everywhere. ~ISAAC ASIMOV

"New ideas pass through three periods:
• It can't be done.
• It probably can be done, but it's not worth doing.
• I knew it was a good idea all along !" ~Arthur C. Clarke.

Some fold for the science. Some fold for points. Some fold because everyone else is doing it.
Many fold for a combination of different reasons. To be honest, it does not matter why you fold. Stanford added the points system for several reasons. It is no coincidence that most of the top folding teams are affiliated with overclocking sites. They basically followed marketing 101. The point system give feedback so we can tell how we are doing, and strive to achieve more. The point system creates a means of competition for those that enjoy competition. The point system provides instant feedback for those that want it. Stanfords goal is not the points, but the results. They need the help of as many people as possible. So fold for whatever reason you want to fold. I don’t care, and neither should anyone else.

Quote:

Discovery and Knowedge are like a new born child. Its parents are often the marrage of Hope, Faith, Greed, Competition, Curiosity, or Boredom. And a new born child is always beautiful, no matter how ugly its parents may be. ~Knitelife, overclock.net 2007

**TaiDinh** · 07-14-07

Quote:

In the end, folding will not produce the cure, it has and will continue to produce results for researchers to study.

I would like to know if there have been any discoveries that they found in computer folding proteins?

Overall, good explanation. It answered some of the questions that pops in my head about folding time after time.

MrBungle · 07-14-07

great stuff. +rep

Knitelife · 07-14-07

Quote:

Originally Posted by TaiDinh

I would like to know if there have been any discoveries that they found in computer folding proteins?

Overall, good explanation. It answered some of the questions that pops in my head about folding time after time.

There is a results section on the Stanford site that does list some of the published findings so far.

http://folding.stanford.edu/results.html

With the speed of which computer technology advances, results will likely continue to increase in frequency.

DELL-HATER · 07-18-07

very nice post! Rep +

DH

SZayat · 07-19-07

What a superb post

. I call for a sticky

JacKz5o · 08-14-07

Nice thread

Zeraphil · 08-18-07

In college we have the whole genetics center running fold@home. I'm waiting for my WC setup so I can join the OCN team!

Look for the Society for Bioinformatics, and resources on molecular computational biology. This application helps, it's an active part of science, and if you read more about what is exactly a protein, the wonders and understanding for folding grows!

It is the 3D configuration that the protein has that gives it its functionality. This 3D spatial config is denominated by the amount of amino acids (which can be up to a hundred), which amino acids there are (which are about 20 in total, polar and non polar, acid and basic) and in -what- sequence you encounter them (also, the pH of the enviroment its in as well!)! Take a macromolecule such as a histone. It forms a H2AH2B dimer and a H3H4 tetramer to construct the nucleosomes that compact DNA to about 50,000 times the space of the total unpacked molecule.

If you ask me, that's crazy. So we have a component of 6 proteins, about 135 amino acids in each, 20 possible amino acids in each slot, and in a specific order that gives it that specific 3D form that will fit with a second similar protein, making a dimer, which will interact with a similar four protein complex to fulfill it's job. Do the math. That's a *****load of information, and of all the possible conformations that a single protein can achieve, only a fraction actually give it the structural properties required to carry out its function in any given condition.

All of this makes my head swirl and my heart jump. We take simple activites for granted, but what's behind the opening of a hand or the focusing of our eyes is great and complex is a wonder we can do it at all!!!

Ok... enough of my starry eyed rant. I just love proteomics *sob*

rymn · 09-22-07

points

**mortimersnerd** · 02-10-09

Lets give this a bump

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Is folding worth it, and does it make a difference?

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