Optimization of minimum set of protein–DNA interactions: a quasi exact solution with minimum over-fitting

@inproceedings{Temiz2010OptimizationOM,
  title={Optimization of minimum set of protein–DNA interactions: a quasi exact solution with minimum over-fitting},
  author={Nuri A Temiz and Andrew C. Trapp and Oleg A. Prokopyev and Carlos J. Camacho},
  booktitle={Bioinformatics},
  year={2010}
}
MOTIVATION A major limitation in modeling protein interactions is the difficulty of assessing the over-fitting of the training set. Recently, an experimentally based approach that integrates crystallographic information of C2H2 zinc finger-DNA complexes with binding data from 11 mutants, 7 from EGR finger I, was used to define an improved interaction code (no optimization). Here, we present a novel mixed integer programming (MIP)-based method that transforms this type of data into an optimized… CONTINUE READING

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