Abstract
Background Protein structural alignment plays a key role in defining gold standards for a variety of bioinformatics applications. These include homology assessment, phylogenetic tree construction and multiple sequence alignment evaluation. Our recent findings [1] however showed that superposition methods are rather sensitive to structural variation. To sidestep the problem of alignment variability, golden standards are often derived from the more conserved and ‘trusted’ regions. It therefore remains unclear which
Highlights
Protein structural alignment plays a key role in defining gold standards for a variety of bioinformatics applications
In this study we shed more light on the structural features and functional importance associated with flexible alignment regions
An example of how the alignment of structural motifs can be impacted by tiny structural variations is given by Figure 2, which shows the alignment between a Glutaminyl-tRNA synthetase and a Caspase-8
Summary
Protein structural alignment plays a key role in defining gold standards for a variety of bioinformatics applications. These include homology assessment, phylogenetic tree construction and multiple sequence alignment evaluation. Our recent findings [1] showed that superposition methods are rather sensitive to structural variation. To sidestep the problem of alignment variability, golden standards are often derived from the more conserved and ‘trusted’ regions. Http://www.biomedcentral.com/1471-2105/10/S13/P6 structural elements characterize alignment variability and what functional information these discarded flexible regions entail
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