Computational studies on the structures of cells, proteins, nucleic acids, and small molecules, and their interactions. Overall the direction of his research has been to push toward the comprehension of the functions of large structures, and the incorporation of diverse data.
Data mining is used to assess protein structures and their interactions, to obtain data for improving sequence matching and to identify the important parts for their mechanisms. We developed a standard ways to view interaction energies between residues, based on sets of protein structures, and standard ways for extracting entropies from changes in structures. These approaches have led to useful ways to incorporate structural information into simulations and new ways to incorporate structural information into protein sequence matching.
Protein Dynamics can be extracted from sets of experimental structures, or from simple models. Large-domain motions of proteins are computed with simple inter-connected elastic models. These highly cohesive, cooperative models are most appropriate for considering the largest functional motions of proteins, which are necessarily independent of the structural details. Functional mechanisms for processing proteins or for protein machines can be developed. The methods lend themselves in straightforward ways to the investigation of the motions of extremely large biomolecular assemblages.
Molecular Mechanisms are developed from protein dynamics, by combining the slowest motions into a sequence of events. Important changes to the dynamics are observed when ligands bind or proteins interact with other proteins.
Deleterious Protein Mutants can affect protein stabilities in significant ways, making them either more stable or less stable. The effects of point mutations are complex and require consideration of their structural environment. These interactions affect the allosteric behaviors, with many deleterious mutants interfering with the biological mechanism.