Prof. Bonnie A Berger

Work on protein structure prediction has led to a number of programs for predicting protein folds from primary sequence data, discovering novel sequence-structure motifs, generating near-native decoys, side-chain packing, and threading. Our work in mathematical models of virus shell assembly introduced a local-rules model for explaining the self assembly of viral shells. Our work in genomics has focused primarily on annotating genes, regulatory motifs, and conserved secondary structures through interspecies comparison. Our work in systems biology has resulted in a program that determines the optimal sampling strategy for time-series expression experiments. All of our programs are freely available for academic use.

The group has continued its efforts in protein structure prediction by updating our coiled-coil programs (i.e., Paircoil2, Multicoil2) and ß-structure prediction and modeling programs (BetaWrapPro), in collaboration with the Keating and King labs (MIT Biology) respectively. BetaWrapPro has recently been awarded a Best Structure Poster award at RECOMB 2005. Our work on beta-helices has provided good computational models for prions and amyloids, which are being tested by the Lindquist (Whitehead and MIT) and Gusella (Harvard Med) labs. We are currently applying our expertise in structure prediction and comparative genomics to functional analysis of protein active sites and binding sites. A recent collaboration with the Perrimon lab (Harvard Med) involves the use of RNA interference (RNAi) for the purpose of elucidating protein-protein interaction networks and signalling pathways. We are also exploring the use of structure to enhance the network-centric perspective of biological systems.