Optimal Protein Threading by Cost-Splitting

  title={Optimal Protein Threading by Cost-Splitting},
  author={Philippe Veber and Nicola Yanev and Rumen Andonov and Vincent Poirriez},
In this paper, we use integer programming approach for solving a hard combinatorial optimization problem, namely protein threading. For this sequence-to-structure alignment problem we apply costsplitting technique to derive a new Lagrangian dual formulation. The optimal solution of the dual is sought by an algorithm of polynomial complexity. For most of the instances the dual solution provides an optimal or near-optimal (with negligible duality gap) alignment. The speed-up with respect to the… CONTINUE READING
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