Algorithm engineering for optimal alignment of protein structure distance matrices

Inken Wohlers 1, * Rumen Andonov 2 Gunnar W. Klau 1
* Corresponding author
2 SYMBIOSE - Biological systems and models, bioinformatics and sequences
IRISA - Institut de Recherche en Informatique et Systèmes Aléatoires, Inria Rennes – Bretagne Atlantique
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.
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Submitted on : Friday, April 15, 2011 - 10:53:19 AM
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Inken Wohlers, Rumen Andonov, Gunnar W. Klau. Algorithm engineering for optimal alignment of protein structure distance matrices. Optimization Letters, Springer Verlag, 2011, ⟨10.1007/s11590-011-0313-3⟩. ⟨inria-00586067⟩

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