Protein design is a young and rapidly growing field. It brings together the expertise of chemists, physicists, mathematicians, and biologists to create the final product: a newly designed protein. Scientists in the field are faced with a fascinating challenge: to outdo Nature in designing proteins. The task is complicated by the fact that natural proteins have undergone millions of years of evolutionary adaptation. Designing proteins from scratch is the ultimate test of our understanding of protein folding, structure, and function. More importantly, protein design has many potential applications in nanotechnology, bioelectronics, industrial chemistry, and medicine.
We use very fast computational algorithms to search through an astronomical number of possible amino acid sequences and to obtain the optimal sequence for a particular protein scaffold. Computationally predicted sequences are constructed experimentally and assayed for the desired properties. Experimental results are fed back into the computational algorithm, completing the protein design cycle. We are particularly interested in applying protein design to studying protein-protein interactions and modifying protein binding affinity and specificity. The nature of our research allows us to work closely with hard-core theorists whose simple models of protein folding and design offer clear insights into protein behavior. At the same time, we collaborate with experimental biologists providing them with computational means to study various biological systems.