There is a volunteer computing project going on right now called “Social Docking” that is written entirely using HTML5 and is run completely within the web browser. It’s an initiative to find compounds of pharmaceutical interest towards AIDS and Alzheimers. All you have to do is visit this HTML5 app socialdocking.appspot.com and let the app be in your browser for about 10 minutes before closing it. You can open a new window to browse the web or do whatever you want on your computer during that time. The idea is to get the simulation to run for 3000 iterations. This low cost supercomputing project will help researchers study three molecules including, HIV-1 integrase, which is a promising target for an AIDS vaccine.
The advantage of socialdocking.appspot.com is that it is web-browser based (as opposed to client-based Folding@Home, SETI@Home, which use BOINC). It also integrates as a Facebook app at http://apps.facebook.com/
Here is more on the science behind this great HTML5 app from the app’s creator Eric Jang.
Developing new drugs is super expensive. It takes a billion dollars and years of clinical trials for company like Pfizer to roll out a new drug into the market. One way that these companies save a lot of time and money is to use Virtual Screening – instead of testing every possible drug candidate in a test tube, they refine a massive database of chemicals by simulating the molecular physics that go on when a drug binds to a receptor. This is called the lock and key model, which states that if a ligand binds strongly to a receptor, it is likely to induce some kind of change with the receptor, and hopefully to some beneficial effect within the cell.
For this project, I am studying three molecules at the same time and trying to find ligands that bind strongly to them. The blue one on the left is HIV-1 integrase, which is a promising target for an AIDS vaccine because it is critical for the HIV virus integrate itself into the host’s DNA replication system. The second one is Acetylcholinesterase, which can be targeted for treating Alzheimersand other forms of dementia. Acetylcholinesterase breaks down a neurotransmitter, so I’m interested in targeting the inhibitor domain that hopefully will render Acetylcholinesterase inactive. Finally, the telomeric RNA quadruplex is a unique secondary structure that personally I have been interested in for some time because I’ve done research on the past with telomeres and G-quadruplexes. It would be really interesting to find some kind of chemical side chain that binds to the arm loops and can allow us to study its role in telomerase regulation and find out more about the topology of quadruplexes.