Journal Article

FZJ-2023-01480

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png TopEnzyme: a framework and database for structural coverage of the functional enzyme space

van der Weg, K. J.FZJ* ; Gohlke, H. (Corresponding author)FZJ*

2023
Oxford Univ. Press Oxford

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Please use a persistent id in citations: http://hdl.handle.net/2128/34219  doi:10.1093/bioinformatics/btad116

Abstract: MotivationTopEnzyme 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.ResultsWe 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.

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Contributing Institute(s):

1. Jülich Supercomputing Center (JSC)
2. Bioinformatik (IBG-4)
3. John von Neumann - Institut für Computing (NIC)

Research Program(s):

1. 5111 - Domain-Specific Simulation & Data Life Cycle Labs (SDLs) and Research Groups (POF4-511) (POF4-511)
2. 2171 - Biological and environmental resources for sustainable use (POF4-217) (POF4-217)
3. Forschergruppe Gohlke (hkf7_20200501) (hkf7_20200501)

Appears in the scientific report 2023

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Database coverage:
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