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October 2009


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Jyh-Ming Lien <[log in to unmask]>
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Jyh-Ming Lien <[log in to unmask]>
Fri, 30 Oct 2009 07:07:22 -0400
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[Apologies for multiple postings]

*    GRAND Seminar


Computing structural changes in proteins


12:00 noon, November 3rd, Tuesday, 2009, ENGR 4201


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


Amarda Shehu


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-defined 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.


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.

*Jyh-Ming Lien*
Assistant Professor, George Mason University