DoSA: Database of Structural Alignments.

Swapnil Mahajan 1, 2, 3 Garima Agarwal 2 Mohammed Iftekhar 2, 4 Bernard Offmann 5 Alexandre De Brevern 1, 3, 6 Narayanaswamy Srinivasan 7, *
* Auteur correspondant
1 DSIMB Réunion - Dynamique des Structures et Interactions des Macromolécules Biologiques- Pôle de La Réunion
DSIMB - Dynamique des Structures et Interactions des Macromolécules Biologiques, UR - Université de la Réunion : UMR_S665
2 Molecular Biophysics Unit
3 GR-Ex, Laboratoire d'Excellence
4 National Center for Biological Sciences
5 UFIP - Fonctionnalité et Ingénierie des Protéines
6 DSIMB - Dynamique des Structures et Interactions des Macromolécules Biologiques
7 MBU
Molecular Biophysics Unit
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/
keyword : protein structure protein structure superimposition optimisation CLUSTALW iPBA substitution matrix PALI database
Type de document :
Article dans une revue
Database (Weston, Conn.) (Weston, Conn.), Oxford Journals, 2013, 2013, pp.bat048. 〈10.1093/database/bat048〉
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Swapnil Mahajan, Garima Agarwal, Mohammed Iftekhar, Bernard Offmann, Alexandre De Brevern, et al.. DoSA: Database of Structural Alignments.. Database (Weston, Conn.) (Weston, Conn.), Oxford Journals, 2013, 2013, pp.bat048. 〈10.1093/database/bat048〉. 〈inserm-00926452〉

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