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

Karel J van der Weg; Holger Gohlke

doi:10.1093/bioinformatics/btad116

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

Bioinformatics. 2023 Mar 1;39(3):btad116. doi: 10.1093/bioinformatics/btad116.

Authors

Karel J van der Weg¹, Holger Gohlke^{1

2}

Affiliations

¹ John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
² Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany.

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/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Protein
Proteins* / chemistry

Substances

Proteins