Protein threading: From mathematical models to parallel implementations

Protein threading: From mathematical models to parallel implementations

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Article ID: iaor2007231
Country: United States
Volume: 16
Issue: 4
Start Page Number: 393
End Page Number: 405
Publication Date: Sep 2004
Journal: INFORMS Journal On Computing
Authors: , ,
Keywords: networks, programming: integer
Abstract:

This paper presents a new network-flow formulation for the problem of predicting 3D protein structures using threading. Several integer-programming models based on this formulation are proposed and compared. These models allow for an efficient decomposition and for the application of a parallel branch-and-cut algorithm, significantly reducing the running time. The efficiency of our approach has been confirmed by extensive computational experiments.

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