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.