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Large-Scale Linear Programming Techniques for the Design of Protein Folding Potentials

Michael Wagner (mwagner***at***odu.edu)
Jaroslaw Meller (jmeller***at***chmcc.org)
Ron Elber (ron***at***cs.cornell.edu)

Abstract: We present large-scale 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 ab-initio} 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 interior-point 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: ODU-TR-2002-02, Department of Mathematics and Statistics, Old Dominion University, Norfolk, VA 23529-0077.

Download: [Compressed Postscript][PDF]

Entry Submitted: 02/12/2002
Entry Accepted: 02/12/2002
Entry Last Modified: 02/12/2002

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