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TopEnzyme: a framework and database for structural coverage of the functional enzyme space
MOTIVATION: TopEnzyme is a database of structural enzyme models created with TopModel and is linked to the SWISS-MODEL repository and AlphaFold Protein Structure Database to provide an overview of structural coverage of the functional enzyme space for over 200 000 enzyme models. It allows the user t...
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/PMC10023222/ https://www.ncbi.nlm.nih.gov/pubmed/36883717 http://dx.doi.org/10.1093/bioinformatics/btad116 |
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author | van der Weg, Karel J Gohlke, Holger |
author_facet | van der Weg, Karel J Gohlke, Holger |
author_sort | van der Weg, Karel J |
collection | PubMed |
description | MOTIVATION: TopEnzyme is a database of structural enzyme models created with TopModel and is linked to the SWISS-MODEL repository and AlphaFold Protein Structure Database to provide an overview of structural coverage of the functional enzyme space for over 200 000 enzyme models. It allows the user to quickly obtain representative structural models for 60% of all known enzyme functions. RESULTS: We assessed the models with TopScore and contributed 9039 good-quality and 1297 high-quality structures. Furthermore, we compared these models to AlphaFold2 models with TopScore and found that the TopScore differs only by 0.04 on average in favor of AlphaFold2. We tested TopModel and AlphaFold2 for targets not seen in the respective training databases and found that both methods create qualitatively similar structures. When no experimental structures are available, this database will facilitate quick access to structural models across the currently most extensive structural coverage of the functional enzyme space within Swiss-Prot. AVAILABILITY AND IMPLEMENTATION: We provide a full web interface to the database at https://cpclab.uni-duesseldorf.de/topenzyme/. |
format | Online Article Text |
id | pubmed-10023222 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-100232222023-03-18 TopEnzyme: a framework and database for structural coverage of the functional enzyme space van der Weg, Karel J Gohlke, Holger Bioinformatics Original Paper MOTIVATION: TopEnzyme is a database of structural enzyme models created with TopModel and is linked to the SWISS-MODEL repository and AlphaFold Protein Structure Database to provide an overview of structural coverage of the functional enzyme space for over 200 000 enzyme models. It allows the user to quickly obtain representative structural models for 60% of all known enzyme functions. RESULTS: We assessed the models with TopScore and contributed 9039 good-quality and 1297 high-quality structures. Furthermore, we compared these models to AlphaFold2 models with TopScore and found that the TopScore differs only by 0.04 on average in favor of AlphaFold2. We tested TopModel and AlphaFold2 for targets not seen in the respective training databases and found that both methods create qualitatively similar structures. When no experimental structures are available, this database will facilitate quick access to structural models across the currently most extensive structural coverage of the functional enzyme space within Swiss-Prot. AVAILABILITY AND IMPLEMENTATION: We provide a full web interface to the database at https://cpclab.uni-duesseldorf.de/topenzyme/. Oxford University Press 2023-03-08 /pmc/articles/PMC10023222/ /pubmed/36883717 http://dx.doi.org/10.1093/bioinformatics/btad116 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 van der Weg, Karel J Gohlke, Holger TopEnzyme: a framework and database for structural coverage of the functional enzyme space |
title | TopEnzyme: a framework and database for structural coverage of the functional enzyme space |
title_full | TopEnzyme: a framework and database for structural coverage of the functional enzyme space |
title_fullStr | TopEnzyme: a framework and database for structural coverage of the functional enzyme space |
title_full_unstemmed | TopEnzyme: a framework and database for structural coverage of the functional enzyme space |
title_short | TopEnzyme: a framework and database for structural coverage of the functional enzyme space |
title_sort | topenzyme: a framework and database for structural coverage of the functional enzyme space |
topic | Original Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10023222/ https://www.ncbi.nlm.nih.gov/pubmed/36883717 http://dx.doi.org/10.1093/bioinformatics/btad116 |
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