Abstract
Protein structure alignment is a crucial step in protein structure–function analysis. Despite the advances in protein structure alignment algorithms, some of the local conformationally similar regions are mislabeled as structurally variable regions (SVRs). These regions are not well superimposed because of differences in their spatial orientations. The Database of Structural Alignments (DoSA) addresses this gap in identification of local structural similarities obscured in global protein structural alignments by realigning SVRs using an algorithm based on protein blocks. A set of protein blocks is a structural alphabet that abstracts protein structures into 16 unique local structural motifs. DoSA provides unique information about 159 780 conformationally similar and 56 140 conformationally dissimilar SVRs in 74 705 pairwise structural alignments of homologous proteins. The information provided on conformationally similar and dissimilar SVRs can be helpful to model loop regions. It is also conceivable that conformationally similar SVRs with conserved residues could potentially contribute toward functional integrity of homologues, and hence identifying such SVRs could be helpful in understanding the structural basis of protein function.Database URL: http://bo-protscience.fr/dosa/
Highlights
Protein structure comparison is an important step in improving our understanding of the mechanistic basis of function of a protein
Database of Structural Alignments (DoSA) is complementary to existing structural alignment databases, and it aims at identifying genuine conformationally similar substructures in regions that are otherwise tagged as structurally variable in these databases
DoSA can aid in providing clues to model loop regions, for which a homologue of similar length is unavailable [17]
Summary
Protein structure comparison is an important step in improving our understanding of the mechanistic basis of function of a protein. The Database of Structural Alignments (DoSA) is a result of our previous work on identification of structurally similar SVRs in homologous proteins by using a PB substitution matrix combined with the modified CLUSTALW [22] algorithm [for more details refer to [17]]. DoSA provides improved structure-based sequence alignments of homologous proteins especially focusing on the SVRs. This database proposes a refined view of the SVRs, which may contain local similarity concealed in global alignment of homologous protein structures.
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