Biology – Quantitative Biology – Quantitative Methods
Scientific paper
2011-04-15
Optimization Letters (2011)
Biology
Quantitative Biology
Quantitative Methods
Scientific paper
10.1007/s11590-011-0313-3
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.
Andonov Rumen
Klau Gunnar W.
Wohlers Inken
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