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| Jed Pitera, Research Staff Member, IBM Almaden Research Center |
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| Dr. Pitera is a research staff member in Science and Technology at the IBM Almaden Research Center. His research focuses on the use of computer simulation to address questions in biology and chemistry, particularly in the areas of protein folding, molecular recognition, and self-assembly. Since February of 2001 Dr. Pitera has worked as a member of the IBM Blue Gene Project Science and Application team. Dr. Pitera received undergraduate training in Biology and Chemistry at the California Institute of Technology, where he worked in Dr. Pamela Bjorkman’s protein crystallography group. Subsequently, he pursued graduate studies in Biophysics at the University of California, San Francisco in the laboratory of Dr. Peter Kollman. In Dr. Kollman’s group, he developed an interest in the use of biomolecular simulation and free energy calculations in the rational design of proteins and pharmaceuticals. He pursued similar work in a postdoctoral position with Prof. Dr. Wilfred van Gunsteren at the ETH in Zurich, Switzerland, where his research focused on novel methods to calculate free energies for ligand design. Dr. Pitera is also an adjunct professor in the UCSF Department of Pharmaceutical Chemistry, and maintains active collaborations with groups at UCSF and Stanford.
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Protein modelling: simulating the thermodynamics and kinetics of protein folding
Jed Pitera, Ph.D., Research Staff Member, IBM Almaden Research Center, San Jose, CA 95120 USA
The IBM Blue Gene project is a large scale multi-year research project to develop a next-generation supercomputer and use it to study the protein folding problem. An overview of the Blue Gene science program will be provided. This program consists of kinetic and thermodynamic simulations of protein folding aimed at answering two questions --first, what chemical interactions drive proteins to fold? and second, how do those interactions control the rate of protein folding? Understanding the protein folding problem could significantly change the process of drug discovery, and will have significant implications for the design of new materials. The ability of current simulation technology to model the effects of mutations on folding will also be discussed.
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