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Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust
Department of Mathematics, Rose-Hulman Institute of Technology, Terre Haute, IN 47803, USA
Roche Diagnostics, Indianapolis, IN 46256, USA
* Author to whom correspondence should be addressed.
Received: 3 October 2013; in revised form: 23 October 2013 / Accepted: 8 November 2013 / Published: 20 November 2013
Abstract: Several efficient algorithms to conduct pairwise comparisons among large databases of protein structures have emerged in the recent literature. The central theme is the design of a measure between the Cα atoms of two protein chains, from which dynamic programming is used to compute an alignment. The efficiency and efficacy of these algorithms allows large-scale computational studies that would have been previously impractical. The computational study herein shows that the structural alignment algorithm eigen-decomposition alignment with the spectrum (EIGAs) is robust against both parametric and structural variation.
Keywords: protein alignment; structural bioinformatics; dynamic programming
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Holder, A.; Simon, J.; Strauser, J.; Taylor, J.; Shibberu, Y. Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust. Biology 2013, 2, 1296-1310.
Holder A, Simon J, Strauser J, Taylor J, Shibberu Y. Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust. Biology. 2013; 2(4):1296-1310.
Holder, Allen; Simon, Jacqueline; Strauser, Jonathon; Taylor, Jonathan; Shibberu, Yosi. 2013. "Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust." Biology 2, no. 4: 1296-1310.