Dataset Information

TopEnzyme: a framework and database for structural coverage of the functional enzyme space.

ABSTRACT:

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/.

SUBMITTER: van der Weg KJ

PROVIDER: S-EPMC10023222 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Publications

TopEnzyme: a framework and database for structural coverage of the functional enzyme space.

van der Weg Karel J KJ Gohlke Holger H

Bioinformatics (Oxford, England) 20230301 3

<h4>Motivation</h4>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.<h4>Results</h4>We assessed the models with TopScore and contributed 9039 good-quality and 1297 high-qual ...[more]

PMID: 36883717

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Dataset Information

TopEnzyme: a framework and database for structural coverage of the functional enzyme space.

Motivation

Results

Availability and implementation

Publications

TopEnzyme: a framework and database for structural coverage of the functional enzyme space.

Similar Datasets

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