Systems Biology of Aromatic Compound Catabolism in Facultative Anaerobic EbN1.

Members of the genus thrive in diverse habitats and use a broad range of recalcitrant organic molecules coupled to denitrification or O respiration. To gain a holistic understanding of the model organism EbN1, we studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate, and acetate utilized under nitrate-reducing versus oxic conditions. Integrated multi-omics (transcriptome, proteome, and metabolome) covered most of the catabolic network (199 genes) and allowed for the refining of knowledge of the degradation modules studied.

BRENDA, the ELIXIR core data resource in 2021: new developments and updates.

The BRENDA enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data.

BRENDA in 2019: a European ELIXIR core data resource.

The BRENDA enzyme database (www.brenda-enzymes.org), recently appointed ELIXIR Core Data Resource, is the main enzyme and enzyme-ligand information system.

BRENDA in 2017: new perspectives and new tools in BRENDA.

The BRENDA enzyme database (www.brenda-enzymes.org) has developed into the main enzyme and enzyme-ligand information system in its 30 years of existence.

BRENDA in 2015: exciting developments in its 25th year of existence.

The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools.

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme portal (http://www.brenda-enzymes.org) is the main information system of functional biochemical and molecular enzyme data and provides access to seven interconnected databases.

BRENDA, the enzyme information system in 2011.

The BRENDA (BRaunschweig ENzyme Database, http://www.brenda-enzymes.org) enzyme information system is the main collection of enzyme functional and property data for the scientific community.

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources.

BTO, the BRENDA Tissue Ontology (http://www.BTO.brenda-enzymes.

Enzyme databases.

Enzymes are catalysts for the chemical reactions in the metabolism of all organisms and play a key role in the regulation of metabolic steps within the cells, as drug targets, and in a wide range of biotechnological applications. With respect to reaction type, they are grouped into six classes, namely oxidoreductases, transferases, hydrolases, lyases, and ligases. EC-Numbers are assigned by the IUBMB.

Automatic assignment of EC numbers.

A wide range of research areas in molecular biology and medical biochemistry require a reliable enzyme classification system, e.g., drug design, metabolic network reconstruction and system biology.

Automatic assignment of reaction operators to enzymatic reactions.

Background: Enzymes are classified in a numerical classification scheme introduced by the Nomenclature Committee of the IUBMB based on the overall reaction chemistry. Due to the manifold of enzymatic reactions the system has become highly complex. Assignment of enzymes to the enzyme classes requires a detailed knowledge of the system and manual analysis.

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009.

The BRENDA (BRaunschweig ENzyme DAtabase) (http://www.brenda-enzymes.org) represents the largest freely available information system containing a huge amount of biochemical and molecular information on all classified enzymes as well as software tools for querying the database and calculating molecular properties.

BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme information system (http://www.brenda.uni-koeln.

BRENDA, the enzyme database: updates and major new developments.

BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature. The database contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers. BRENDA includes biochemical and molecular information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation and preparation, links and literature references.

BRENDA: a resource for enzyme data and metabolic information.

BRENDA (BRaunschweig ENzyme DAtabase), founded in 1987 by Dietmar Schomburg, is a comprehensive protein function database, containing enzymatic and metabolic information extracted from the primary literature. Presently, the database holds data on more than 40 000 enzymes and 4460 different organisms, and includes information about enzyme-ligand relationships with numerous chemical compounds. The collection of molecular and biochemical information in BRENDA provides a fundamental resource for research in biotechnology, pharmacology, medicinal diagnostics, enzyme mechanics, and metabolism.

BRENDA, enzyme data and metabolic information.

BRENDA is a comprehensive relational database on functional and molecular information of enzymes, based on primary literature. The database contains information extracted and evaluated from approximately 46 000 references, holding data of at least 40 000 different enzymes from more than 6900 different organisms, classified in approximately 3900 EC numbers. BRENDA is an important tool for biochemical and medical research covering information on properties of all classified enzymes, including data on the occurrence, catalyzed reaction, kinetics, substrates/products, inhibitors, cofactors, activators, structure and stability.