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

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

1
Department of Mathematics, Rose-Hulman Institute of Technology, Terre Haute, IN 47803, USA
2
Roche Diagnostics, Indianapolis, IN 46256, USA
*
Author to whom correspondence should be addressed.
Received: 3 October 2013 / Revised: 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 (CC BY 3.0).

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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.

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