ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information
The formation of a stable complex between proteins lies at the core of a wide variety of biological processes and has been the focus of countless experiments. The huge amount of information contained in the protein structural interactome in the Protein Data Bank can now be used to characterise and c...
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ftpubmed:oai:pubmedcentral.nih.gov:10771469 2024-02-11T10:00:42+01:00 ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information Giulini, Marco Honorato, Rodrigo V. Rivera, Jesús L. Bonvin, Alexandre M. J. J. 2024-01-06 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10771469/ http://www.ncbi.nlm.nih.gov/pubmed/38184711 https://doi.org/10.1038/s42003-023-05718-w en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10771469/ http://www.ncbi.nlm.nih.gov/pubmed/38184711 http://dx.doi.org/10.1038/s42003-023-05718-w © The Author(s) 2024 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . Commun Biol Article Text 2024 ftpubmed https://doi.org/10.1038/s42003-023-05718-w 2024-01-14T01:51:17Z The formation of a stable complex between proteins lies at the core of a wide variety of biological processes and has been the focus of countless experiments. The huge amount of information contained in the protein structural interactome in the Protein Data Bank can now be used to characterise and classify the existing biological interfaces. We here introduce ARCTIC-3D, a fast and user-friendly data mining and clustering software to retrieve data and rationalise the interface information associated with the protein input data. We demonstrate its use by various examples ranging from showing the increased interaction complexity of eukaryotic proteins, 20% of which on average have more than 3 different interfaces compared to only 10% for prokaryotes, to associating different functions to different interfaces. In the context of modelling biomolecular assemblies, we introduce the concept of “recognition entropy”, related to the number of possible interfaces of the components of a protein-protein complex, which we demonstrate to correlate with the modelling difficulty in classical docking approaches. The identified interface clusters can also be used to generate various combinations of interface-specific restraints for integrative modelling. The ARCTIC-3D software is freely available at github.com/haddocking/arctic3d and can be accessed as a web-service at wenmr.science.uu.nl/arctic3d. Text Arctic PubMed Central (PMC) Arctic Communications Biology 7 1 |
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Article Giulini, Marco Honorato, Rodrigo V. Rivera, Jesús L. Bonvin, Alexandre M. J. J. ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information |
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The formation of a stable complex between proteins lies at the core of a wide variety of biological processes and has been the focus of countless experiments. The huge amount of information contained in the protein structural interactome in the Protein Data Bank can now be used to characterise and classify the existing biological interfaces. We here introduce ARCTIC-3D, a fast and user-friendly data mining and clustering software to retrieve data and rationalise the interface information associated with the protein input data. We demonstrate its use by various examples ranging from showing the increased interaction complexity of eukaryotic proteins, 20% of which on average have more than 3 different interfaces compared to only 10% for prokaryotes, to associating different functions to different interfaces. In the context of modelling biomolecular assemblies, we introduce the concept of “recognition entropy”, related to the number of possible interfaces of the components of a protein-protein complex, which we demonstrate to correlate with the modelling difficulty in classical docking approaches. The identified interface clusters can also be used to generate various combinations of interface-specific restraints for integrative modelling. The ARCTIC-3D software is freely available at github.com/haddocking/arctic3d and can be accessed as a web-service at wenmr.science.uu.nl/arctic3d. |
format |
Text |
author |
Giulini, Marco Honorato, Rodrigo V. Rivera, Jesús L. Bonvin, Alexandre M. J. J. |
author_facet |
Giulini, Marco Honorato, Rodrigo V. Rivera, Jesús L. Bonvin, Alexandre M. J. J. |
author_sort |
Giulini, Marco |
title |
ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information |
title_short |
ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information |
title_full |
ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information |
title_fullStr |
ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information |
title_full_unstemmed |
ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information |
title_sort |
arctic-3d: automatic retrieval and clustering of interfaces in complexes from 3d structural information |
publisher |
Nature Publishing Group UK |
publishDate |
2024 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10771469/ http://www.ncbi.nlm.nih.gov/pubmed/38184711 https://doi.org/10.1038/s42003-023-05718-w |
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Arctic |
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Arctic |
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Arctic |
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Arctic |
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Commun Biol |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10771469/ http://www.ncbi.nlm.nih.gov/pubmed/38184711 http://dx.doi.org/10.1038/s42003-023-05718-w |
op_rights |
© The Author(s) 2024 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
op_doi |
https://doi.org/10.1038/s42003-023-05718-w |
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Communications Biology |
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7 |
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