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Michael Wagner (mwagnerodu.edu) Abstract: We present largescale optimization techniques to model the energy function that underlies the folding process of proteins. Linear Programming is used to identify parameters in the energy function model, the objective being that the model predict the structure of known proteins correctly. Such trained functions can then be used either for {\em abinitio} prediction or for recognition of unknown structures. In order to obtain good energy models we need to be able to solve dense Linear Programming Problems with tens (possibly hundreds) of millions of constraints in a few hundred parameters, which we achieve by tailoring and parallelizing the interiorpoint code PCx. Keywords: protein folding potentials, linear programming, parallel processing, linear inequality systems Category 1: Applications  Science and Engineering (Basic Sciences Applications ) Category 2: Linear, Cone and Semidefinite Programming (Linear Programming ) Category 3: Optimization Software and Modeling Systems (Parallel Algorithms ) Citation: ODUTR200202, Department of Mathematics and Statistics, Old Dominion University, Norfolk, VA 235290077. Download: [Compressed Postscript][PDF] Entry Submitted: 02/12/2002 Modify/Update this entry  
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