Folding Proteins at Home
Imagine if nobody cared to help better mankind and we had no knowledge of the human body. Medicine would be a thing of ritual blood lettings and diseases that could not be cured. Today we know better that in order to find cures for many diseases we have to know more about the human body and things like the human genome and protein folding. The human genome project was a bold enterprise to help discover more about humans and their genes. They discovered more about the human body and helped to discuss and address the social, legal and ethical issues of the project as well as the important medical parts. Folding proteins is a next logical step to help learn even more about the human DNA, genes and diseases.
“Proteins are nature’s workhorses, it’s nanomachines.” From the folding@home website. Proteins are simply the human and all other living organisms biochemical workers. Some proteins form the walls of our cells while others carry messages or speed up chemical reactions. Proteins perform an interesting and as yet not fully understood action before it can do it’s work. A protein will fold in a precise manner or form before it goes about its work. It needs to do this and it will do it perfectly to perform the job it is supposed to, and it will fold in a particular shape and way.
But if it does not fold into the shape or form it needs to we get a misfold or what becomes a disease. Diseases that occur from these misfolds are tragic and difficult to cure. Things like Alzheimer’s, Parkinson’s, and Mad Cow are some of the many that we know about. We need to know more about protein folding and to do this scientists at universities need to test and experiment to discover more. They can experiment using computers to emulate or copy the process of folding but to do this they would need super computers or lots of regular computers. This is where the average person with a computer and internet connection can come in.
I have been folding proteins on my computer for a couple of days and already processed one fold, whatever that means. I am not exactly sure what they are doing as far as copying the process but my computer is being used while I am not using it to fold the proteins in an experiment.
The whole process is called distributed computing and it is a great way for a university like Stanford to conduct experiments like this. They simply create a server system to use people’s computers to run small portions of computational programs to solve the problems they want to. They break down the programs into ones that one computer can do on its own and send it out over the internet. The computers that are part of the experiment download the main program that will run in the background of your computer and use whatever parts of your computers processor you are not using.
Think about all the times during the day that you are not using your computer but it is on. I know we have ours on from the time we get up in the morning to late at night and there is plenty of time that I am not using it or only using a small portion of the processor. I have checked and before the program was installed on my desktop the processor was using from 4 to 8 percent of the processor when I was on the internet researching or checking my mail.
As I type this the folding program is running and I cannot tell other than the icon on the task bar. It does not slow down my computer, it simply uses the processor when I am not. The program runs as slow or as fast depending on how much of the processor it can use at any given time. When you use more of your processor it uses less and will slow down the folding program. If you want to make sure that your processor is totally available while you use your computer for something like a video game or video editing you can simply right click the icon on the task bar and shut it down. When you reboot your computer the program will start up again or you can restart it by go into your program file menu and click on the menu item for folding@home there.
To understand why a university or research team would need the help of so many other people to simulate a protein folding I will refer you to a short description they give on their web page.
“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!”
What this really means in terms I can understand is it would take a lot of computers to simulate one protein folding. It takes a long time for computers to simulate what happens in a short time in real life so they need to have lots of computers to break this down and accomplish the simulations in a realistic time frame. This is accomplished through the use of hundreds of thousands and millions of personal computers over the internet.
And you can be a part of this really useful experiment. I am sure many people want to help out and this is a great way for the average person to do just that. Leave a legacy for your children and help mankind. Join the growing trend in small people making a difference in a great way and participate in folding@home. Go to the folding at home website here for more information, results of the experiments and to download your part of the worldwide search for cures to many of mankinds diseases.
Stanford Universities folding at home: http://folding.stanford.edu/
