The Effective Fragment Potential simulation method being perfected using Alliance resources will help researchers overcome one of the biggest challenges in modeling proteins-size.
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The Effective Fragment Potential simulation method being perfected using Alliance resources will help researchers overcome one of the biggest challenges in modeling proteins-size. |
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The thousands of proteins that exist inside cells of all living organisms are made from just 20 amino acids that must fold in very specific patterns in order to function properly. That much scientists know. What scientists don't know is precisely how these complex molecules do their job—how they form and break bonds to catalyze the necessary reactions that sustain life. As University of Iowa theoretical chemist Jan Jensen puts it, "We often don't know what exactly is going on inside proteins."
To Jensen, the inside of a protein is the electrostatic environment of the individual atoms and the strongly polar nature that this environment creates in the constituent amino acids. Jensen and his research group use NCSA's SGI Origin2000 supercomputer—and, previously, the IBM SP supercomputer at the Maui High Performance Computing Center, an Alliance Partner for Advanced Computational Services—to model how these electrostatic charges affect protein bonding activity. 
Jensen's research team at the University of Iowa includes Ryan Minikis, Pablo Molina, Hui Li, and Visvaldas Kairys (now at the Center for Advanced Research in Biotechnology). "We are trying to get down to the physics of how the molecules interact," Jensen says.
Jan Jensen, Pablo Molina, Hui Li, and Ryan Minikis. Access Online | Posted 7-18-2000 |
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