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ICARUS: flexible protein structural alignment based on Protein Units
MOTIVATION: Alignment of protein structures is a major problem in structural biology. The first approach commonly used is to consider proteins as rigid bodies. However, alignment of protein structures can be very complex due to conformational variability, or complex evolutionary relationships betwee...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10400377/ https://www.ncbi.nlm.nih.gov/pubmed/37498544 http://dx.doi.org/10.1093/bioinformatics/btad459 |
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author | Cretin, Gabriel Périn, Charlotte Zimmermann, Nicolas Galochkina, Tatiana Gelly, Jean-Christophe |
author_facet | Cretin, Gabriel Périn, Charlotte Zimmermann, Nicolas Galochkina, Tatiana Gelly, Jean-Christophe |
author_sort | Cretin, Gabriel |
collection | PubMed |
description | MOTIVATION: Alignment of protein structures is a major problem in structural biology. The first approach commonly used is to consider proteins as rigid bodies. However, alignment of protein structures can be very complex due to conformational variability, or complex evolutionary relationships between proteins such as insertions, circular permutations or repetitions. In such cases, introducing flexibility becomes useful for two reasons: (i) it can help compare two protein chains which adopted two different conformational states, such as due to proteins/ligands interaction or post-translational modifications, and (ii) it aids in the identification of conserved regions in proteins that may have distant evolutionary relationships. RESULTS: We propose ICARUS, a new approach for flexible structural alignment based on identification of Protein Units, evolutionarily preserved structural descriptors of intermediate size, between secondary structures and domains. ICARUS significantly outperforms reference methods on a dataset of very difficult structural alignments. AVAILABILITY AND IMPLEMENTATION: Code is freely available online at https://github.com/DSIMB/ICARUS. |
format | Online Article Text |
id | pubmed-10400377 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-104003772023-08-05 ICARUS: flexible protein structural alignment based on Protein Units Cretin, Gabriel Périn, Charlotte Zimmermann, Nicolas Galochkina, Tatiana Gelly, Jean-Christophe Bioinformatics Original Paper MOTIVATION: Alignment of protein structures is a major problem in structural biology. The first approach commonly used is to consider proteins as rigid bodies. However, alignment of protein structures can be very complex due to conformational variability, or complex evolutionary relationships between proteins such as insertions, circular permutations or repetitions. In such cases, introducing flexibility becomes useful for two reasons: (i) it can help compare two protein chains which adopted two different conformational states, such as due to proteins/ligands interaction or post-translational modifications, and (ii) it aids in the identification of conserved regions in proteins that may have distant evolutionary relationships. RESULTS: We propose ICARUS, a new approach for flexible structural alignment based on identification of Protein Units, evolutionarily preserved structural descriptors of intermediate size, between secondary structures and domains. ICARUS significantly outperforms reference methods on a dataset of very difficult structural alignments. AVAILABILITY AND IMPLEMENTATION: Code is freely available online at https://github.com/DSIMB/ICARUS. Oxford University Press 2023-07-27 /pmc/articles/PMC10400377/ /pubmed/37498544 http://dx.doi.org/10.1093/bioinformatics/btad459 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Paper Cretin, Gabriel Périn, Charlotte Zimmermann, Nicolas Galochkina, Tatiana Gelly, Jean-Christophe ICARUS: flexible protein structural alignment based on Protein Units |
title | ICARUS: flexible protein structural alignment based on Protein Units |
title_full | ICARUS: flexible protein structural alignment based on Protein Units |
title_fullStr | ICARUS: flexible protein structural alignment based on Protein Units |
title_full_unstemmed | ICARUS: flexible protein structural alignment based on Protein Units |
title_short | ICARUS: flexible protein structural alignment based on Protein Units |
title_sort | icarus: flexible protein structural alignment based on protein units |
topic | Original Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10400377/ https://www.ncbi.nlm.nih.gov/pubmed/37498544 http://dx.doi.org/10.1093/bioinformatics/btad459 |
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