Fast protein structure alignment

Authors:
Yosi Shibberu;Allen Holder;Kyla Lutz
Affiliations:
Department of Mathematics, Rose-Hulman Institute of Technology;Department of Mathematics, Rose-Hulman Institute of Technology;Department of Mathematics, Rose-Hulman Institute of Technology
Venue:
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
Year:
2010

Citing 5
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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.