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

Abstract The BRENDA enzyme database (https://www.brenda-enzymes.org), established in 1987, has evolved into the main collection of functional enzyme and metabolism data. In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the integration of newly discovered enzymes. The main part contains >5 million data for ∼90 000 enzymes from ∼13 000 organisms, manually extracted from ∼157 000 primary literature references, combined with information of text and data mining, data integration, and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, genome annotations, ligand information, taxonomic, bibliographic, and kinetic data. BRENDA offers an easy access to enzyme information from quick to advanced searches, text- and structured-based queries for enzyme-ligand interactions, word maps, and visualization of enzyme data. The BRENDA Pathway Maps are completely revised and updated for an enhanced interactive and intuitive usability. The new design of the Enzyme Summary Page provides an improved access to each individual enzyme. A new protein structure 3D viewer was integrated. The prediction of the intracellular localization of eukaryotic enzymes has been implemented. The new EnzymeDetector combines BRENDA enzyme annotations with protein and genome databases for the detection of eukaryotic and prokaryotic enzymes.

[1]  Rida Assaf,et al.  Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center , 2016, Nucleic Acids Res..

[2]  W SEWELL,et al.  MEDICAL SUBJECT HEADINGS IN MEDLARS. , 1964, Bulletin of the Medical Library Association.

[3]  Antje Chang,et al.  BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA , 2012, Nucleic Acids Res..

[4]  Antje Chang,et al.  The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources , 2010, Nucleic Acids Res..

[5]  Silvio C. E. Tosatto,et al.  InterPro in 2019: improving coverage, classification and access to protein sequence annotations , 2018, Nucleic Acids Res..

[6]  Antje Chang,et al.  BRENDA in 2017: new perspectives and new tools in BRENDA , 2016, Nucleic Acids Res..

[7]  David A. Lee,et al.  CATH: comprehensive structural and functional annotations for genome sequences , 2014, Nucleic Acids Res..

[8]  Lei Shi,et al.  SABIO-RK—database for biochemical reaction kinetics , 2011, Nucleic Acids Res..

[9]  Steven E Brenner,et al.  SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. , 2017, Journal of molecular biology.

[10]  Tanya Z. Berardini,et al.  The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments , 2013, J. Biomed. Semant..

[11]  Evan Bolton,et al.  Database resources of the National Center for Biotechnology Information , 2017, Nucleic Acids Res..

[12]  Carol Edwards,et al.  Integration of Genomic and Medical Data into a 3D Atlas of Human Anatomy , 2008, MMVR.

[13]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[14]  S. Brunak,et al.  Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. , 2000, Journal of molecular biology.

[15]  Robert Petryszak,et al.  The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences , 2020, Bioinformatics.

[16]  Antje Chang,et al.  BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009 , 2008, Nucleic Acids Res..

[17]  Scott Federhen,et al.  The NCBI Taxonomy database , 2011, Nucleic Acids Res..

[18]  Antje Chang,et al.  BRENDA in 2019: a European ELIXIR core data resource , 2018, Nucleic Acids Res..

[19]  David S. Goodsell,et al.  RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy , 2018, Nucleic Acids Res..

[20]  Antje Chang,et al.  BRENDA in 2015: exciting developments in its 25th year of existence , 2014, Nucleic Acids Res..

[21]  Antje Chang,et al.  Development of a classification scheme for disease-related enzyme information , 2011, BMC Bioinformatics.

[22]  Dietmar Schomburg,et al.  A metabolite-centric view on flux distributions in genome-scale metabolic models , 2013, BMC Systems Biology.

[23]  Minoru Kanehisa,et al.  KEGG: new perspectives on genomes, pathways, diseases and drugs , 2016, Nucleic Acids Res..

[24]  Erik L. L. Sonnhammer,et al.  A Hidden Markov Model for Predicting Transmembrane Helices in Protein Sequences , 1998, ISMB.

[25]  S. Rosanoff,et al.  An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge , 2017, Protein engineering, design & selection : PEDS.

[26]  Dietmar Schomburg,et al.  BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation , 2017, PloS one.

[27]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[28]  Andrew G. McDonald,et al.  ExplorEnz: the primary source of the IUBMB enzyme list , 2008, Nucleic Acids Res..

[29]  David S. Goodsell,et al.  The RCSB protein data bank: integrative view of protein, gene and 3D structural information , 2016, Nucleic Acids Res..

[30]  Wen J. Li,et al.  Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation , 2015, Nucleic Acids Res..

[31]  Markus Krummenacker,et al.  The MetaCyc database of metabolic pathways and enzymes , 2017, Nucleic acids research.

[32]  Leyla Jael García Castro,et al.  Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data , 2013, Journal of Biomedical Semantics.

[33]  The UniProt Consortium,et al.  UniProt: a worldwide hub of protein knowledge , 2018, Nucleic Acids Res..

[34]  Christian Ebeling,et al.  BacDive – The Bacterial Diversity Metadatabase in 2016 , 2015, Nucleic Acids Res..