My research group is involved both in fundamental methods development research and in trying to fight disease more directly. Most of the information on this site focuses on basic research, but I thought you might be interested in hearing about some of the disease related work we are doing.

Malaria: We are part of a collaborative project headed by Austin Burt at Imperial College in London that is one of the Gates Foundation "Grand Challenge Projects in Global Health". Malaria is caused by a parasite that spends part of its life cycle inside the mosquito, and is passed along to humans by mosquito bites. The idea behind the project is to make mosquitos resistant to the parasite by eliminating genes required in the mosquito for the parasite to live. Our part of the project is to use our computer based design methods (rosetta) to engineer new enzymes that will specifically target and inactivate these genes.

Anthrax: We are helping a research group at Harvard build models of anthrax toxin that should contribute to the development of treatments. You can read the abstract of a paper describing some of this work at
http://www.pnas.org/cgi/content/abstract/102/45/16409

HIV: One of the reasons that HIV is such a deadly virus is that it has evolved to trick the immune system. We are collaborating with researchers in Seattle and at the NIH to try to develop a vaccine for HIV. Our role in this project is central--we are using rosetta to design small proteins that display the small number of critical regions of the HIV coat protein in a way that the immune system can easily recognize and generate antibodies to. Our goal is to create small stable protein vaccines that can be made very cheaply and shipped all over the world.

You might wonder what the relationship is between protein structure prediction and designing new proteins. It turns out they are very closely related, and the improvments in methods you are helping us make can be directly translated into making new enzymes, vaccines, etc. For more information on protein design you might be interested in looking at the review we recently wrote in science which is available at our home page (depts.washington.edu/bakerpg)
Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., Baker, D. (2005). Progress in modeling of protein structures and interactions Science 310, 638-642. [Full Text PDF]

With the wonderful contributions all of you are making, we can now make much more rapid progress on the disease fighting front. David Kim is working on an internal queuing system so that the scientists in my group working on these projects can utilize this amazing new resource. Right now he is the only one who can submit jobs, which is a hassle for him especially since there are so many other aspects of keeping the project going he is working on every day. So be on the lookout for new types of work units several weeks from now.

Thanks again for all your help, and happy thanksgiving!

David