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

Autor: Alexandre G. de Brevern, Sylvain Leonard, Agnel Praveen Joseph, Jean-Christophe Gelly, Narayanaswamy Srinivasan
Přispěvatelé: Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), GR-Ex, Laboratoire d'Excellence, GR-Ex, Molecular Biophysics Unit, Indian Institute of Science, Indo-French collaborative grant (CEFIPRA/IFCPAR 3903-E) 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), de Brevern, Alexandre G.
Jazyk: angličtina
Rok vydání: 2014
Předmět:
Models
Molecular
Web server
Protein Conformation
Computer science
Structural alignment
MESH: Sequence Alignment
computer.software_genre
webserver
03 medical and health sciences
MESH: Software
MESH: Protein Conformation
Structural Biology
Iterative refinement
[SDV.BBM] Life Sciences [q-bio]/Biochemistry
Molecular Biology
MESH: Proteins
[SDV.BBM]Life Sciences [q-bio]/Biochemistry
Molecular Biology
Loop modeling
protein conformations
protein superimposition
Molecular Biology
Java applet
030304 developmental biology
Internet
0303 health sciences
Multiple sequence alignment
030302 biochemistry & molecular biology
Computational Biology
Proteins
General Medicine
computer.file_format
Protein structure prediction
Protein Data Bank
Crystallography
MESH: Internet
protein structures
Protein Blocks
structural alphabet
Sequence Alignment
computer
Algorithm
Software
MESH: Models
Molecular
MESH: Computational Biology
Zdroj: Journal of Biomolecular Structure and Dynamics
Journal of Biomolecular Structure and Dynamics, Taylor & Francis: STM, Behavioural Science and Public Health Titles, 2014, 32 (4), pp.661-8. ⟨10.1080/07391102.2013.787026⟩
ISSN: 0739-1102
1538-0254
DOI: 10.1080/07391102.2013.787026⟩
Popis: International audience; 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/ .
Databáze: OpenAIRE
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