Seminar - Computing Structural Changes in Proteins
Date: March 6, 2009
Time: 4:00 PM
Location: Matheson Hall, Room: 109
Nurit Haspel, PhD
Department of Computer Science
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 and while most proteins have a well-defined three-dimensional structure, they undergo structural changes as part of their function. Understanding the structure and dynamics of proteins is crucial for understanding the processes they mediate. Various computational methods exist for modeling and simulating protein structure and dynamics. These methods have a wide variety of applications in modeling and determining protein structures, designing novel structures, explaining protein-protein interactions and more. In the first part of the talk, Dr. Haspel will present the application of Molecular Dynamic (MD) simulations to the design and analysis of novel nano-structures based on the self-assembly of segments from existing protein structures.
In the second part of the talk, Dr. Haspel will present methods for exploring the dynamics of proteins on larger time scales. 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. Two novel search methods will be discussed, aimed to characterize the structure, dynamics and flexibility of protein structures at various levels of details: the first is a hybrid method that combines an efficient robotics-inspired sampling algorithm with small scale, detailed simulations to characterize the local dynamics of proteins. The second is a fast, approximate search method that samples large scale structural changes in proteins.
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Dr. Haspel is a postdoctoral research associate in Lydia Kavraki's Physical and biological computing group at Rice university. She graduated from the Department of Computer Science in Tel Aviv University, Israel, where she was a member of the structural bioinformatics group. Her advisors were Prof. Ruth Nussinov and Prof. Haim Wolfson. More details can be found in her CV.
Dr. Haspel's research lies in the areas of computational structural biology and structural bioinformatics, with the goal of better understanding the structure and flexibility of proteins, to model conformational changes in proteins, and to design novel nano-structures that may contribute to the understanding of the self-assembly properties of proteins and facilitate experimental nano-design. The focus of her research is on both the development of novel algorithms and the application of state-of-the-art existing methodologies to various problems in molecular biology, nanobiology and biochemistry. A detailed description of Dr. Haspel's past and present research can be found here.
Matheson Hall is located at 32nd and Market Streets.