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Algorithm engineering for optimal alignment of protein structure distance matrices
Abstract : Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring function. We introduce the structural alignment problem formally, which enables us to express a variety of scoring functions used in previous work as special cases in a unified framework. Further, we propose the first mathematical model for computing optimal structural alignments based on dense inter-residue distance matrices. We therefore reformulate the problem as a special graph problem and give a tight integer linear programming model. We then present algorithm engineering techniques to handle the huge integer linear programs of real-life distance matrix alignment problems. Applying these techniques, we can compute provably optimal Dali alignments for the very first time.
Cited literature [25 references]
https://hal.inria.fr/inria-00586067
Contributor : Inken Wohlers Connect in order to contact the contributor
Submitted on : Friday, April 15, 2011 - 10:53:19 AM
Last modification on : Friday, February 4, 2022 - 3:19:40 AM
Long-term archiving on: : Saturday, July 16, 2011 - 2:30:23 AM
Contributor : Inken Wohlers Connect in order to contact the contributor
Submitted on : Friday, April 15, 2011 - 10:53:19 AM
Last modification on : Friday, February 4, 2022 - 3:19:40 AM
Long-term archiving on: : Saturday, July 16, 2011 - 2:30:23 AM
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