Alexandre G. de Brevern's publications
Year 2014
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Léonard S.*, Joseph A.P.*, Srinivasan N., Gelly J.-C., de Brevern A.G.#
mulPBA : an efficient multiple protein structure alignment method based on a structural alphabet
J Biol Struct Dyn (2014) in press.
The increasing number of available protein structures requires efficient tools for multiple structure comparison. Indeed, multiple structural alignments are essential for the analysis of function, evolution and architecture of protein structures. For this purpose, we proposed a new web server called multiple Protein Block Alignment (mulPBA). This server implements a method based on a structural alphabet to describe the backbone conformation of a protein chain in terms of dihedral angles. This ‘sequence-like’ representation enables the use of powerful sequence alignment methods for primary structure comparison, followed by an iterative refinement of the structural superposition. This approach yields alignments superior to most of the rigid-body alignment methods and highly comparable with the flexible structure comparison approaches. We implement this method in a web server designed to do multiple structure superimpositions from a set of structures given by the user. Outputs are given as both sequence alignment and superposed 3D structures visualized directly by static images generated by PyMol or through a Jmol applet allowing dynamic interaction. Multiple global quality measures are given. Relatedness between structures is indicated by a distance dendogram. Superimposed structures in PDB format can be also downloaded, and the results are quickly obtained. mulPBA server can be accessed at .
preprint
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collaboration with Pr. N. Srinivasan of Molecular Biophysics Unit (IISc, India). Funding:- Indo-French collaborative grant (CEFIPRA/IFCPAR 3903-E) [link to the project]
- The Ministry of Research (France)
- The University Paris Diderot, Sorbonne Paris Cite (France)
- The National Institute of Blood Transfusion (INTS, France)
- The National Institute of Health and Medical Research (INSERM, France)
- The Laboratories of Excellence, GR-Ex (France)
- Department of Biotechnology (India)
Alexandre G. de Brevern
Last Modification : January 2014
