Research Interests

The research in my group combines computational biophysics and bioinformatics with the goal of understanding the structural, physical and chemical basis of a wide range of biological phenomena. Our work includes fundamental theoretical research, the development of software tools, and applications to problems of biological importance. For some time we have been developing methods that allow us to calculate the forces that drive fundamental biological processes. Electrostatic potentials and free energies are obtained from numerical solutions of the Poisson-Boltzmann (PB) equation calculated with the DelPhi and GRASP programs developed in our lab. These terms are then integrated into a methodology where other forces are obtained from standard molecular mechanics methods, yielding a complete expression for conformational and binding free energies of almost any system of interest. The methodology is under constant development and refinement, often driven by new applications. Areas of current interest include protein structure prediction and understanding the structural origins of specificity in protein-protein, protein-membrane and protein-DNA interactions. Specific applications of our methods include the study of specificity determinants in cadherins that play a central role in cell-cell interactions, the recognition by transcription factors of different DNA sequences, and the structural origins of protein targeting to specific biological membranes.

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Primary Section

Section 29: Biophysics and Computational Biology

Secondary Section

Section 21: Biochemistry