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mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet

Leonard, Sylvain and Joseph, Agnel Praveen and Srinivasan, Narayanaswamy and Gelly, Jean-Christophe and de Brevern, Alexandre G (2014) mulPBA: an efficient multiple protein structure alignment method based on a structural alphabet. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32 (4). pp. 661-668.

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Official URL: http://dx.doi.org/10.1080/07391102.2013.787026

Abstract

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 www.dsimb.inserm.fr/dsimb_tools/mulpba/.

Item Type: Journal Article
Additional Information: Copyright for this article belongs to the TAYLOR & FRANCIS INC,USA
Keywords: amino acid; structural alphabet; Protein Blocks; progressive sequence alignment strategy; semi-global alignment; anchor-based alignment; protein folds; structural comparison; Protein Data Bank
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Depositing User: Id for Latest eprints
Date Deposited: 17 Feb 2014 11:07
Last Modified: 17 Feb 2014 11:07
URI: http://eprints.iisc.ac.in/id/eprint/48406

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