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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ftunivutrecht:oai:dspace.library.uu.nl:1874/437114 2024-04-14T08:06:58+00:00 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. Sub NMR Spectroscopy NMR Spectroscopy 2024-01-06 application/pdf https://dspace.library.uu.nl/handle/1874/437114 en eng 2399-3642 https://dspace.library.uu.nl/handle/1874/437114 info:eu-repo/semantics/OpenAccess Medicine (miscellaneous) General Biochemistry,Genetics and Molecular Biology General Agricultural and Biological Sciences Article 2024 ftunivutrecht 2024-03-27T15:03:51Z 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. Article in Journal/Newspaper Arctic Utrecht University Repository Arctic |
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collection |
Utrecht University Repository |
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ftunivutrecht |
language |
English |
topic |
Medicine (miscellaneous) General Biochemistry,Genetics and Molecular Biology General Agricultural and Biological Sciences |
spellingShingle |
Medicine (miscellaneous) General Biochemistry,Genetics and Molecular Biology General Agricultural and Biological Sciences 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 |
topic_facet |
Medicine (miscellaneous) General Biochemistry,Genetics and Molecular Biology General Agricultural and Biological Sciences |
description |
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. |
author2 |
Sub NMR Spectroscopy NMR Spectroscopy |
format |
Article in Journal/Newspaper |
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 |
publishDate |
2024 |
url |
https://dspace.library.uu.nl/handle/1874/437114 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_relation |
2399-3642 https://dspace.library.uu.nl/handle/1874/437114 |
op_rights |
info:eu-repo/semantics/OpenAccess |
_version_ |
1796304195058401280 |