Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

Joseph, Agnel Praveen and Srinivasan, Narayanaswamy and de Brevern, Alexandre G (2012) Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies. In: BIOCHIMIE, 94 (9). pp. 2025-2034.

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Abstract

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a ID sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. (C) 2012 Elsevier Masson SAS. All rights reserved.

Item Type:	Journal Article
Publication:	BIOCHIMIE
Publisher:	ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER
Additional Information:	Copyright for this article belongs to Elsevier
Keywords:	Protein structure comparison; Structural alphabet; Protein Blocks; Anchor-based alignment; Protein structure mining; Protein Data Bank; Structure conservation
Department/Centre:	Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited:	17 Sep 2012 10:33
Last Modified:	17 Sep 2012 10:33
URI:	http://eprints.iisc.ac.in/id/eprint/45062

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