Computing structural changes in proteins

12:00 noon, November 03, Tuesday, 2009, ENGR 4201

Speaker

Nurit Haspel
Assistant Professor
Department of Computer Science
University of Massachusetts Boston

Abstract

Proteins are involved in virtually every process and aspect in life ? from the flexing of our muscles to our immune system response. It is widely accepted that proteins are dynamic molecules with generally well-defiined three-dimensional structures, and that understanding the structure and dynamics of proteins is crucial for understanding their function and the processes they mediate. Various computational methods exist for modeling and simulating protein structure and dynamics, but several traditional methods are limited due to the large amount of calculations involved. This talk will present a number of methods for searching the conformational space of proteins at various time and space scales. On the one end of the spectrum, Molecular Dynamics calculations are used for detailed analysis of local structural changes in proteins. On the other end, robotics-inspired search techniques are used to characterize the structure and dynamics of proteins by representing them using a mechanistic/geometric models subject to physics constraints.

Short Bio

Nurit Haspel is an assistant professor in the department of Computer Science at the University of Massachusetts in Boston. She received her BSc. in Chemistry and Computer Science from Tel Aviv University and her Masters and Ph.D in Structural Bioinformatics (Computer Science) from Tel Aviv University in 2007. She did her postdoctoral research in the department of Computer Science at Rice University in Houston, TX. Her research involves developing and applying computational methods to explore the structure and dynamics of protein molecules. Some applications include the computational design of nano-structures, applying computational simulations and search techniques to understand aspects of the human immune system inhibition and developing algorithms taken from Robotics and graph theory to simulate large scale structural changes in protein complexes.