A Generalized Threading Model Using Integer Programming that Allows for Secondary Structure Element Deletion

Kyle Ellrott[1] (kellrott@csbl.bmb.uga.edu)
Jun-tao Guo[1],[2] (guy@csbl.bmb.uga.edu)
Victor Olman[1] (olman@bmb.uga.edu)
Ying Xu[1],[2] (xyn@bmb.uga.edu)

[1]Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30622, USA
[2]Institute of Bioinformatics, University of Georgia, 120 Green St, Athens, GA 30602, USA


Abstract

Integer programming is a combinatorial optimization method that has been successfully applied to the protein threading problem. We seek to expand the model optimized by this technique to allow for a more accurate description of protein threading. We have developed and implemented an expanded model of integer programming that has the capability to model secondary structure element deletion, which was not possible in previous version of integer programming based optimization.

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Japanese Society for Bioinformatics