The Physics department colloquia are usually on Friday afternoons at 3 pm in Room 135. Coffee and cookies are served at 2:45 pm in the same room. Anyone is welcome.

Computational Methods for Protein Structure Prediction, Protein Dynamics and Drug Discovery
Dr. Steffen Lindert, Post Doctoral Researcher, Department of Pharmacology, University of California-San Diego

Computational methods are very useful for investigating biological systems. In addition to simulating molecular scale events that may not be probed easily by experiment, simulations can also inform experiments and vice versa. Here, three main computational methods are applied to probe biological processes and systems: molecular dynamics, de novo protein structure prediction using sparse experimental restraints, and computer-aided drug discovery. More specifically, molecular dynamics methods are used to investigate the opening and closing properties of the hydrophobic patch in Troponin C, an important process in the contraction of heart muscle cells. Furthermore, the development of EM-Fold, a software tool to fold proteins into medium resolution cryoEM density maps is presented. EM-Fold is able to predict the structure of large helical proteins with atomic detail. Finally, the relaxed complex scheme, a computer-aided drug discovery method accounting for receptor flexibility, was used to find potent inhibitions of two enzymes involved in bacterial cell wall synthesis. The lead compound was shown to be effective in animal models and to have synergistic activity with methicillin.