Computational biochemistry and genomics

Modeling protein structures / designing novel folds
We are developing a computational approach to model proteins for which a limited number of experimental restraints are available. We utilize our recently developed fragment library of supersecondary structure elements (Smotifs) that was shown to have saturated almost 10 years ago. We hypothesize that all protein folds should be possible to build from this library. We are developing algorithms that take advantage of NMR checial shift information to identify a subset of Smotifs that form a protein and setting up optimization approaches that will rapidly assemble overlapping Smotifs into compact folds.

Structural genomics / receptor-ligand interaction of IGSF proteins

As members of the New York Structural Genomics Center and the Immune Function Network we are exploring a variety of biomedical topics from a structral biology point of view. We are particularly interested in the cell surface costimulatory and inhibitory immunoglobulin superfamily proteins that effect immunity and tolerance responses. We are interested in understanding of the molecular level recognition mechanisms of these receptor ligand systems.

Evolution of robustness in gene networks / protein-DNA interactions

Previous research has shown gene regulatory networks are robust to perturbations at the level of the connections between transcription factors. We investigate the mechanisms underlying the evolution of robustness in gene networks using a modeling approach, which considers three levels: binding of individual transcription factors to DNA, dynamics of gene expression levels, and fitness effects at the population level.