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Biology 2013, 2(4), 1296-1310; doi:10.3390/biology2041296
Article

Dynamic Programming Used to Align Protein Structures with a Spectrum Is Robust

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Received: 3 October 2013; in revised form: 23 October 2013 / Accepted: 8 November 2013 / Published: 20 November 2013
(This article belongs to the Special Issue Developments in Bioinformatic Algorithms)
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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 protein alignment; structural bioinformatics; dynamic programming
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

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.

AMA Style

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.

Chicago/Turabian Style

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.



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