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Protein threading is a method of computational protein structure predictionused for protein sequences which have the same fold as proteins of knownstructures but do not have homologous proteins with known structure. The mostpopular algorithm is based on linear integer programming. In this paper, weconsider methods based on nonlinear integer programming. Actually, the existinglinear integer programming is directly linearized from the original quadraticinteger programming. We then develop corresponding efficient algorithms.

Protein Threading Based on Nonlinear Integer Programming