What If?
What if there was a cure for cancer in your lifetime? What if Alzheimer’s was a thing of the past?
What if redirecting wasted computing power could make these lofty dreams a reality? What if harnessing all that power was easy to do? What if you were part of the solution? What if you could personally benefit while contributing a little time to a cause so much bigger than yourself?
What is Protein Folding and Why Does It Matter?
Protein folding is the physical process by which a protein chain takes the shape necessary to perform a function in the human body, for example as part of cellular structure or as an antibody. It is central to healthy biological processes.
Cancer and Alzheimer’s (among others) are well-known proteopathic3 diseases, in which certain proteins become structurally abnormal, or misfolded. Scientists and medical researchers alike investigate why the proteins misfold and how medicines can be designed to correct the process. Gaining a deeper understanding of the protein folding process will get the medical community that much closer to curing these horrible diseases that have affected so many. Working the Problem: We Need More Power!
Due to the complexity of proteins’ conformation or configuration space (the set of possible shapes a protein can take), as well as the statistically random, time-based nature of the modeling, it is exceptionally difficult to scale these simulations using general-purpose supercomputers. Such systems are intrinsically costly and typically shared among many research groups. So, how do researchers even begin to solve this massive computational problem? Enter distributed computing.
The Internet emerged as a consumer phenomenon in the late 1990’s and early 2000’s. Soon after, scientific investigators found applications for distributing massively parallel computing jobs to individual consumers. Consumers could install software provided by the scientific investigator onto their own computers and leave the machines powered on even when not actively using them. The scientific investigators would use the leftover computing cycles to assist in solving their scientific problems. An early example was Distributed.net4 founded in 1997. The initial problem they investigated was the mathematical principle of the “Golomb ruler”. Once the 27 and 28 mark Golomb rulers were solved, they moved on to trying to break the RC5-72 encryption standard. They remain active and expect to take 200 years to exhaust the RC5-72 key space. Berkley’s BOINC5 is another example of a network with thousands of participants. However, there is one distributed computing project of particular interest in the fight against cancer.
Folding Coin whitepaper