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 cl...
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Veröffentlicht in: | Nucleic acids research 2021-01, Vol.49 (D1), p.D498-D508 |
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description | 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. |
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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.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkaa1025</identifier><identifier>PMID: 33211880</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Acetyl Coenzyme A - biosynthesis ; Arabidopsis - enzymology ; Bacillus subtilis - enzymology ; Database Issue ; Databases, Protein ; Enzymes - chemistry ; Imaging, Three-Dimensional ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Search Engine</subject><ispartof>Nucleic acids research, 2021-01, Vol.49 (D1), p.D498-D508</ispartof><rights>The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 2021</rights><rights>The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c482t-411c64de076b56993863c2c2f20a8247fd4886c5de7a9b707ed312d750d094fc3</citedby><cites>FETCH-LOGICAL-c482t-411c64de076b56993863c2c2f20a8247fd4886c5de7a9b707ed312d750d094fc3</cites><orcidid>0000-0002-2176-8751</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779020/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779020/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33211880$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chang, Antje</creatorcontrib><creatorcontrib>Jeske, Lisa</creatorcontrib><creatorcontrib>Ulbrich, Sandra</creatorcontrib><creatorcontrib>Hofmann, Julia</creatorcontrib><creatorcontrib>Koblitz, Julia</creatorcontrib><creatorcontrib>Schomburg, Ida</creatorcontrib><creatorcontrib>Neumann-Schaal, Meina</creatorcontrib><creatorcontrib>Jahn, Dieter</creatorcontrib><creatorcontrib>Schomburg, Dietmar</creatorcontrib><title>BRENDA, the ELIXIR core data resource in 2021: new developments and updates</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>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.</description><subject>Acetyl Coenzyme A - biosynthesis</subject><subject>Arabidopsis - enzymology</subject><subject>Bacillus subtilis - enzymology</subject><subject>Database Issue</subject><subject>Databases, Protein</subject><subject>Enzymes - chemistry</subject><subject>Imaging, Three-Dimensional</subject><subject>Metabolic Networks and Pathways</subject><subject>Molecular Sequence Annotation</subject><subject>Search Engine</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kE1P20AQQFdVqxJCb5yrvZUDbmY_7LV7qAQh0IgIJEQlbqvN7hjcOl53107Fv8dRCIILpznM05vRI-SQwXcGhZg0Jkzu_xrDgKcfyIiJjCeyyPhHMgIBacJA5ntkP8Y_AEyyVH4me0JwxvIcRuTy9GZ2dXZyTLsHpLPF_G5-Q60PSJ3pDA0YfR8s0qqhHDj7QRv8Tx2usfbtCpsuUtM42rcDjfGAfCpNHfHL8xyT3-ez2-mvZHF9MZ-eLBIrc94lkjGbSYegsmWaFYXIM2G55SUHk3OpSifzPLOpQ2WKpQKFTjDuVAoOCllaMSY_t962X67Q2eGPYGrdhmplwqP2ptJvN031oO_9WiulCuAwCI6eBcH_6zF2elVFi3VtGvR91Fxmgg2xYIMeb1EbfIwBy5czDPSmvx76613_Af_6-rUXeBd8AL5tAd-376ueAIe0jSI</recordid><startdate>20210108</startdate><enddate>20210108</enddate><creator>Chang, Antje</creator><creator>Jeske, Lisa</creator><creator>Ulbrich, Sandra</creator><creator>Hofmann, Julia</creator><creator>Koblitz, Julia</creator><creator>Schomburg, Ida</creator><creator>Neumann-Schaal, Meina</creator><creator>Jahn, Dieter</creator><creator>Schomburg, Dietmar</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0002-2176-8751</orcidid></search><sort><creationdate>20210108</creationdate><title>BRENDA, the ELIXIR core data resource in 2021: new developments and updates</title><author>Chang, Antje ; Jeske, Lisa ; Ulbrich, Sandra ; Hofmann, Julia ; Koblitz, Julia ; Schomburg, Ida ; Neumann-Schaal, Meina ; Jahn, Dieter ; Schomburg, Dietmar</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c482t-411c64de076b56993863c2c2f20a8247fd4886c5de7a9b707ed312d750d094fc3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Acetyl Coenzyme A - biosynthesis</topic><topic>Arabidopsis - enzymology</topic><topic>Bacillus subtilis - enzymology</topic><topic>Database Issue</topic><topic>Databases, Protein</topic><topic>Enzymes - chemistry</topic><topic>Imaging, Three-Dimensional</topic><topic>Metabolic Networks and Pathways</topic><topic>Molecular Sequence Annotation</topic><topic>Search Engine</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chang, Antje</creatorcontrib><creatorcontrib>Jeske, Lisa</creatorcontrib><creatorcontrib>Ulbrich, Sandra</creatorcontrib><creatorcontrib>Hofmann, Julia</creatorcontrib><creatorcontrib>Koblitz, Julia</creatorcontrib><creatorcontrib>Schomburg, Ida</creatorcontrib><creatorcontrib>Neumann-Schaal, Meina</creatorcontrib><creatorcontrib>Jahn, Dieter</creatorcontrib><creatorcontrib>Schomburg, Dietmar</creatorcontrib><collection>Access via Oxford University Press (Open Access Collection)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chang, Antje</au><au>Jeske, Lisa</au><au>Ulbrich, Sandra</au><au>Hofmann, Julia</au><au>Koblitz, Julia</au><au>Schomburg, Ida</au><au>Neumann-Schaal, Meina</au><au>Jahn, Dieter</au><au>Schomburg, Dietmar</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>BRENDA, the ELIXIR core data resource in 2021: new developments and updates</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2021-01-08</date><risdate>2021</risdate><volume>49</volume><issue>D1</issue><spage>D498</spage><epage>D508</epage><pages>D498-D508</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>33211880</pmid><doi>10.1093/nar/gkaa1025</doi><orcidid>https://orcid.org/0000-0002-2176-8751</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Acetyl Coenzyme A - biosynthesis Arabidopsis - enzymology Bacillus subtilis - enzymology Database Issue Databases, Protein Enzymes - chemistry Imaging, Three-Dimensional Metabolic Networks and Pathways Molecular Sequence Annotation Search Engine |
title | BRENDA, the ELIXIR core data resource in 2021: new developments and updates |
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