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.
Biology 2013, 2(4), 1296-1310; https://doi.org/10.3390/biology2041296
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)
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. View Full-Text
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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.