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Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.
Joseph A. P., Srinivasan N., De Brevern A. G.
Biochimie 94, 9 (2012) 2025-34 - http://www.hal.inserm.fr/inserm-00750325
Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies.
Agnel Praveen Joseph1, Narayanaswamy Srinivasan2, Alexandre De Brevern () 1
1 :  DSIMB - Dynamique des Structures et Interactions des Macromolécules Biologiques
INSERM : U665 – INTS – Université Paris Diderot, Sorbonne Paris Cité
6 rue Alexandre Cabanel, 75739 Paris cedex 15
2 :  Molecular Biophysics Unit
Indian Institute of Science
Bangalore 560 012
MULtiple Protein Block Alignment
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 1D 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.
Sciences du Vivant/Biochimie, Biologie Moléculaire
Sciences du Vivant/Bio-Informatique, Biostatistique
Sciences du Vivant/Biochimie, Biologie Moléculaire/Biologie structurale

Articles dans des revues avec comité de lecture
Biochimie (Biochimie)
Publisher Elsevier
ISSN 0300-9084 

protein structure comparison – structural alphabet – Protein Blocks – anchor-based alignment – protein structure mining – Protein Data Bank – structure conservation.
Models – Molecular – Protein Conformation – Proteins – Sequence Alignment – Sequence Homology – Amino Acid
French Ministry of Research, University of Paris Diderot - Paris 7, Sorbone Paris Cité, French National Institute for Blood Transfusion (INTS), French Institute for Health and Medical Research (INSERM), Indian Department of Biotechnology, CEFIPRA/IFCPAR for collaborative grant (number 3903-E).
Liste des fichiers attachés à ce document : 
Joseph_Srinivasan_de_Brevern_Biochimie_2012_preprint.pdf(846 KB)
Joseph_Srinivasan_de_Brevern_Biochimie_2012_preprint-T1.pdf(115.2 KB)
Joseph_Srinivasan_de_Brevern_Biochimie_2012_SupData.pdf(739.5 KB)