{"id":"https://openalex.org/W4323438785","doi":"https://doi.org/10.1093/bioinformatics/btad116","title":"TopEnzyme: a framework and database for structural coverage of the functional enzyme space","display_name":"TopEnzyme: a framework and database for structural coverage of the functional enzyme space","publication_year":2023,"publication_date":"2023-03-01","ids":{"openalex":"https://openalex.org/W4323438785","doi":"https://doi.org/10.1093/bioinformatics/btad116","pmid":"https://pubmed.ncbi.nlm.nih.gov/36883717"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad116","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad116/49555817/btad116.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad116/49555817/btad116.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032889918","display_name":"Karel van der Weg","orcid":"https://orcid.org/0000-0002-1896-0291"},"institutions":[{"id":"https://openalex.org/I171892758","display_name":"Forschungszentrum J\u00fclich","ror":"https://ror.org/02nv7yv05","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I171892758"]},{"id":"https://openalex.org/I4210113364","display_name":"John von Neumann Institute for Computing","ror":"https://ror.org/02zmk8084","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I1305996414","https://openalex.org/I1305996414","https://openalex.org/I169556180","https://openalex.org/I171892758","https://openalex.org/I2801876189","https://openalex.org/I4210113364"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Karel J van der Weg","raw_affiliation_strings":["John von Neumann Institute for Computing (NIC), J\u00fclich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum J\u00fclich GmbH , J\u00fclich 52425, Germany"],"raw_orcid":"https://orcid.org/0000-0002-1896-0291","affiliations":[{"raw_affiliation_string":"John von Neumann Institute for Computing (NIC), J\u00fclich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum J\u00fclich GmbH , J\u00fclich 52425, Germany","institution_ids":["https://openalex.org/I4210113364","https://openalex.org/I171892758"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063949219","display_name":"Holger Gohlke","orcid":"https://orcid.org/0000-0001-8613-1447"},"institutions":[{"id":"https://openalex.org/I171892758","display_name":"Forschungszentrum J\u00fclich","ror":"https://ror.org/02nv7yv05","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I171892758"]},{"id":"https://openalex.org/I4210113364","display_name":"John von Neumann Institute for Computing","ror":"https://ror.org/02zmk8084","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I1305996414","https://openalex.org/I1305996414","https://openalex.org/I169556180","https://openalex.org/I171892758","https://openalex.org/I2801876189","https://openalex.org/I4210113364"]},{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Holger Gohlke","raw_affiliation_strings":["Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225, Germany","John von Neumann Institute for Computing (NIC), J\u00fclich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum J\u00fclich GmbH , J\u00fclich 52425, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8613-1447","affiliations":[{"raw_affiliation_string":"Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University D\u00fcsseldorf , D\u00fcsseldorf 40225, Germany","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"John von Neumann Institute for Computing (NIC), J\u00fclich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum J\u00fclich GmbH , J\u00fclich 52425, Germany","institution_ids":["https://openalex.org/I4210113364","https://openalex.org/I171892758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5063949219"],"corresponding_institution_ids":["https://openalex.org/I171892758","https://openalex.org/I4210113364","https://openalex.org/I44260953"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3204,"currency":"EUR","value_usd":3455},"fwci":0.8722,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.73719177,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"39","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.27900001406669617,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.27900001406669617,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.24549999833106995,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.18469999730587006,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6144052743911743},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.5196736454963684},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4149303436279297},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3374525308609009},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32714641094207764}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6144052743911743},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.5196736454963684},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4149303436279297},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3374525308609009},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32714641094207764},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad116","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad116/49555817/btad116.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36883717","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36883717","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10023222","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10023222","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10023222/pdf/btad116.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad116","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad116","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad116/49555817/btad116.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.44999998807907104}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4323438785.pdf"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1965827393","https://openalex.org/W1995808589","https://openalex.org/W2021639324","https://openalex.org/W2027687260","https://openalex.org/W2097632784","https://openalex.org/W2101220662","https://openalex.org/W2111973517","https://openalex.org/W2121704271","https://openalex.org/W2122536720","https://openalex.org/W2140673705","https://openalex.org/W2143011057","https://openalex.org/W2157848815","https://openalex.org/W2159614853","https://openalex.org/W2166637863","https://openalex.org/W2171419407","https://openalex.org/W2894445194","https://openalex.org/W2910475706","https://openalex.org/W2950954328","https://openalex.org/W2963703197","https://openalex.org/W2996561088","https://openalex.org/W3000866803","https://openalex.org/W3092932912","https://openalex.org/W3106745904","https://openalex.org/W3112376646","https://openalex.org/W3141162744","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3211597279","https://openalex.org/W3211795435","https://openalex.org/W4234714728","https://openalex.org/W4251926840","https://openalex.org/W4281790889","https://openalex.org/W6684606845","https://openalex.org/W6751037545"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"MOTIVATION:":[0],"TopEnzyme":[1],"is":[2,13],"a":[3,156],"database":[4,129,162],"of":[5,28,31,54,97,144],"structural":[6,29,50,135,142],"enzyme":[7,34,40,57,147],"models":[8,51,63,78,81,136],"created":[9],"with":[10,64,82],"TopModel":[11,101],"and":[12,19,66,70,84,102,113],"linked":[14],"to":[15,24,46,79,134,160],"the":[16,32,44,62,87,109,138,145,161],"SWISS-MODEL":[17],"repository":[18],"AlphaFold":[20],"Protein":[21],"Structure":[22],"Database":[23],"provide":[25,155],"an":[26],"overview":[27],"coverage":[30,143],"functional":[33,146],"space":[35,148],"for":[36,52,104],"over":[37],"200":[38],"000":[39],"models.":[41],"It":[42],"allows":[43],"user":[45],"quickly":[47],"obtain":[48],"representative":[49],"60%":[53],"all":[55],"known":[56],"functions.":[58],"RESULTS:":[59],"We":[60,99,154],"assessed":[61],"TopScore":[65,83,88],"contributed":[67],"9039":[68],"good-quality":[69],"1297":[71],"high-quality":[72],"structures.":[73,121],"Furthermore,":[74],"we":[75],"compared":[76],"these":[77],"AlphaFold2":[80,103],"found":[85,114],"that":[86,115],"differs":[89],"only":[90],"by":[91],"0.04":[92],"on":[93],"average":[94],"in":[95,108],"favor":[96],"AlphaFold2.":[98],"tested":[100],"targets":[105],"not":[106],"seen":[107],"respective":[110],"training":[111],"databases":[112],"both":[116],"methods":[117],"create":[118],"qualitatively":[119],"similar":[120],"When":[122],"no":[123],"experimental":[124],"structures":[125],"are":[126],"available,":[127],"this":[128],"will":[130],"facilitate":[131],"quick":[132],"access":[133],"across":[137],"currently":[139],"most":[140],"extensive":[141],"within":[149],"Swiss-Prot.":[150],"AVAILABILITY":[151],"AND":[152],"IMPLEMENTATION:":[153],"full":[157],"web":[158],"interface":[159],"at":[163],"https://cpclab.uni-duesseldorf.de/topenzyme/.":[164]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
