Even with this procedure, the calculation of the structure of the HDEA protein took 70 hours running on 64 parallel processors of the Cornell Theory Center's IBM SP2 supercomputer. The MarA simulation took 100 hours on the same number of processors.
The Scheraga group includes visiting scientist Adam Liwo, research associates Jooyoung Lee and Jaroslaw Pillardy, and senior research associate Daniel R. Ripoll. They use the Parallel Processing Resource for Biomedical Applications at the Cornell Theory Center, funded by the National Center for Computational Resources at the National Institutes of Health.
The group's approach is described in four papers:
-- J. Lee, A. Liwo and H. A. Scheraga, Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K, Proc. Natl. Acad. Sci., USA, 96, 2025-2030 (1999).
-- A. Liwo, J. Lee, D. R. Ripoll, J. Pillardy and H. A. Scheraga, Protein structure prediction by global optimization of a potential energy function, Proc. Natl. Acad. Sci., USA, 96, 5482-5485 (1999).
-- J. Lee, A. Liwo, D.R. Ripoll, J. Pillardy and H.A. Scheraga, Calculation of protein conformation by global optimization of a potential energy function, Proteins: Structure, Function and Genetics, in press.
-- J. Lee, A. Liwo, D. Ripoll, J. Pillardy, J.A. Saunders, K.D. Gibson and H.A. Scheraga, Hierarchical energy-based approach to protein-structure prediction; blind-test evaluation with CASP3 targets, Intl. J. Quantum Chem., submitted.
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Contact: Bill Steele
ws21@cornell.edu
607-255-7164
Cornell University News Service
29-Jul-1999