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iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach
BACKGROUND: Protein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure superimposition analysis. Multiple approaches have been developed to perform s...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6825713/ https://www.ncbi.nlm.nih.gov/pubmed/31700529 http://dx.doi.org/10.1186/s13029-019-0075-3 |
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author | Faure, Guilhem Joseph, Agnel Praveen Craveur, Pierrick Narwani, Tarun J. Srinivasan, Narayanaswamy Gelly, Jean-Christophe Rebehmed, Joseph de Brevern, Alexandre G. |
author_facet | Faure, Guilhem Joseph, Agnel Praveen Craveur, Pierrick Narwani, Tarun J. Srinivasan, Narayanaswamy Gelly, Jean-Christophe Rebehmed, Joseph de Brevern, Alexandre G. |
author_sort | Faure, Guilhem |
collection | PubMed |
description | BACKGROUND: Protein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure superimposition analysis. Multiple approaches have been developed to perform such task and are often based on structural superimposition deduced from sequence alignment, which does not take into account structural features. Our methodology is based on the use of a Structural Alphabet (SA), i.e. a library of 3D local protein prototypes able to approximate protein backbone. The interest of a SA is to translate into 1D sequences into the 3D structures. RESULTS: We used Protein blocks (PB), a widely used SA consisting of 16 prototypes, each representing a conformation of the pentapeptide skeleton defined in terms of dihedral angles. Proteins are described using PB from which we have previously developed a sequence alignment procedure based on dynamic programming with a dedicated PB Substitution Matrix. We improved the procedure with a specific two-step search: (i) very similar regions are selected using very high weights and aligned, and (ii) the alignment is completed (if possible) with less stringent parameters. Our approach, iPBA, has shown to perform better than other available tools in benchmark tests. To facilitate the usage of iPBA, we designed and implemented iPBAvizu, a plugin for PyMOL that allows users to run iPBA in an easy way and analyse protein superimpositions. CONCLUSIONS: iPBAvizu is an implementation of iPBA within the well-known and widely used PyMOL software. iPBAvizu enables to generate iPBA alignments, create and interactively explore structural superimposition, and assess the quality of the protein alignments. |
format | Online Article Text |
id | pubmed-6825713 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-68257132019-11-07 iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach Faure, Guilhem Joseph, Agnel Praveen Craveur, Pierrick Narwani, Tarun J. Srinivasan, Narayanaswamy Gelly, Jean-Christophe Rebehmed, Joseph de Brevern, Alexandre G. Source Code Biol Med Research BACKGROUND: Protein 3D structure is the support of its function. Comparison of 3D protein structures provides insight on their evolution and their functional specificities and can be done efficiently via protein structure superimposition analysis. Multiple approaches have been developed to perform such task and are often based on structural superimposition deduced from sequence alignment, which does not take into account structural features. Our methodology is based on the use of a Structural Alphabet (SA), i.e. a library of 3D local protein prototypes able to approximate protein backbone. The interest of a SA is to translate into 1D sequences into the 3D structures. RESULTS: We used Protein blocks (PB), a widely used SA consisting of 16 prototypes, each representing a conformation of the pentapeptide skeleton defined in terms of dihedral angles. Proteins are described using PB from which we have previously developed a sequence alignment procedure based on dynamic programming with a dedicated PB Substitution Matrix. We improved the procedure with a specific two-step search: (i) very similar regions are selected using very high weights and aligned, and (ii) the alignment is completed (if possible) with less stringent parameters. Our approach, iPBA, has shown to perform better than other available tools in benchmark tests. To facilitate the usage of iPBA, we designed and implemented iPBAvizu, a plugin for PyMOL that allows users to run iPBA in an easy way and analyse protein superimpositions. CONCLUSIONS: iPBAvizu is an implementation of iPBA within the well-known and widely used PyMOL software. iPBAvizu enables to generate iPBA alignments, create and interactively explore structural superimposition, and assess the quality of the protein alignments. BioMed Central 2019-11-02 /pmc/articles/PMC6825713/ /pubmed/31700529 http://dx.doi.org/10.1186/s13029-019-0075-3 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Faure, Guilhem Joseph, Agnel Praveen Craveur, Pierrick Narwani, Tarun J. Srinivasan, Narayanaswamy Gelly, Jean-Christophe Rebehmed, Joseph de Brevern, Alexandre G. iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach |
title | iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach |
title_full | iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach |
title_fullStr | iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach |
title_full_unstemmed | iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach |
title_short | iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach |
title_sort | ipbavizu: a pymol plugin for an efficient 3d protein structure superimposition approach |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6825713/ https://www.ncbi.nlm.nih.gov/pubmed/31700529 http://dx.doi.org/10.1186/s13029-019-0075-3 |
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