Biological Sciences, Software Engineering
Applications in Life Sciences
Applications in Physical Sciences
I am very lucky to be working with wonderful colleagues on a fascinating problem: how to model biomolecular systems with sufficient accuracy to enable the computation of the structures of the macromolecules which occur in nature from genomic sequences, and the design of a whole new world of macromolecules with new and useful functions. We are making progress but there is still a huge way to go.
To carry out the prediction and design calculations, we have been developing a computer program called Rosetta. At the core of Rosetta are potential functions for computing the energies of interactions within and between macromolecules, and methods for finding the lowest energy structure for a protein or RNA sequence (structure prediction) and for finding the lowest energy sequence for a protein or given structure or function (design).
Aspects of this have been embodied in the web-based videogame Foldit. Recently, several tens of thousands of gamers playing Foldit solved an AIDS-related protein structure problem that had baffled the scientific community for a decade.