Abstract
We address the problem of aligning the 3D structures of two proteins. Our pairwise comparisons are based on a new optimization model that is succinctly expressed in terms of linear transformations and highlights the problem’s intrinsic geometry. The optimization problem is approximately solved with a new polynomial time algorithm. The worst-case analysis of the algorithm shows that the solution is bounded by a constant depending on the data of the problem.
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Shibberu, Y., Holder, A., Lutz, K. (2010). Fast Protein Structure Alignment. In: Borodovsky, M., Gogarten, J.P., Przytycka, T.M., Rajasekaran, S. (eds) Bioinformatics Research and Applications. ISBRA 2010. Lecture Notes in Computer Science(), vol 6053. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13078-6_18
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DOI: https://doi.org/10.1007/978-3-642-13078-6_18
Publisher Name: Springer, Berlin, Heidelberg
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