A two-phase relaxation-based heuristic for the maximum feasible subsystem problem
Computers and Operations Research
Research Article: Global energy minimization of alanine dipeptide via barrier function methods
Computational Biology and Chemistry
Randomized relaxation methods for the maximum feasible subsystem problem
IPCO'05 Proceedings of the 11th international conference on Integer Programming and Combinatorial Optimization
International Journal of Data Mining and Bioinformatics
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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 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.