{"id":"https://openalex.org/W2116976883","doi":"https://doi.org/10.1093/nar/gkr874","title":"eQuilibrator--the biochemical thermodynamics calculator","display_name":"eQuilibrator--the biochemical thermodynamics calculator","publication_year":2011,"publication_date":"2011-11-07","ids":{"openalex":"https://openalex.org/W2116976883","doi":"https://doi.org/10.1093/nar/gkr874","mag":"2116976883","pmid":"https://pubmed.ncbi.nlm.nih.gov/22064852"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkr874","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr874","pdf_url":"https://academic.oup.com/nar/article-pdf/40/D1/D770/9482100/gkr874.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","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/nar/article-pdf/40/D1/D770/9482100/gkr874.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062382712","display_name":"Avi I. Flamholz","orcid":"https://orcid.org/0000-0002-9278-5479"},"institutions":[{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"A. Flamholz","raw_affiliation_strings":["Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel","institution_ids":["https://openalex.org/I53964585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021074279","display_name":"\u0395lad Noor","orcid":"https://orcid.org/0000-0001-8776-4799"},"institutions":[{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"E. Noor","raw_affiliation_strings":["Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100 Israel","Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100 Israel","institution_ids":["https://openalex.org/I53964585"]},{"raw_affiliation_string":"Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel","institution_ids":["https://openalex.org/I53964585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044028530","display_name":"Arren Bar\u2010Even","orcid":"https://orcid.org/0000-0002-1039-4328"},"institutions":[{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"A. Bar-Even","raw_affiliation_strings":["Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100 Israel","Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100 Israel","institution_ids":["https://openalex.org/I53964585"]},{"raw_affiliation_string":"Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel","institution_ids":["https://openalex.org/I53964585"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024451873","display_name":"Ron Milo","orcid":"https://orcid.org/0000-0003-1641-2299"},"institutions":[{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"R. Milo","raw_affiliation_strings":["Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100 Israel","Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100 Israel","institution_ids":["https://openalex.org/I53964585"]},{"raw_affiliation_string":"Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel","institution_ids":["https://openalex.org/I53964585"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5024451873"],"corresponding_institution_ids":["https://openalex.org/I53964585"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.5243,"has_fulltext":true,"cited_by_count":609,"citation_normalized_percentile":{"value":0.95668702,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"40","issue":"D1","first_page":"D770","last_page":"D775"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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/T12763","display_name":"ATP Synthase and ATPases Research","score":0.9973999857902527,"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/T13539","display_name":"thermodynamics and calorimetric analyses","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gibbs-free-energy","display_name":"Gibbs free energy","score":0.7145304083824158},{"id":"https://openalex.org/keywords/calculator","display_name":"Calculator","score":0.6568689346313477},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.5759115815162659},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4995739459991455},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.4784262776374817},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44117826223373413},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.42271921038627625},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.42244088649749756},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4149352014064789},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.26471832394599915},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12798166275024414},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.12440076470375061}],"concepts":[{"id":"https://openalex.org/C146477669","wikidata":"https://www.wikidata.org/wiki/Q334631","display_name":"Gibbs free energy","level":2,"score":0.7145304083824158},{"id":"https://openalex.org/C2776836400","wikidata":"https://www.wikidata.org/wiki/Q31087","display_name":"Calculator","level":2,"score":0.6568689346313477},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.5759115815162659},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4995739459991455},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.4784262776374817},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44117826223373413},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.42271921038627625},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.42244088649749756},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4149352014064789},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.26471832394599915},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12798166275024414},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.12440076470375061},{"id":"https://openalex.org/C58226133","wikidata":"https://www.wikidata.org/wiki/Q1324199","display_name":"Pulmonary surfactant","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C55352822","wikidata":"https://www.wikidata.org/wiki/Q5558978","display_name":"Gibbs isotherm","level":3,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001669","descriptor_name":"Biochemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkr874","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr874","pdf_url":"https://academic.oup.com/nar/article-pdf/40/D1/D770/9482100/gkr874.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:22064852","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22064852","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:escidoc.org:escidoc:2037371","is_oa":false,"landing_page_url":"http://hdl.handle.net/11858/00-001M-0000-0019-DB74-7","pdf_url":null,"source":{"id":"https://openalex.org/S7407052962","display_name":"Max Planck Digital Library","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:open-archive.highwire.org:nar:40/D1/D770","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/40/D1/D770","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:3245061","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3245061","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkr874","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr874","pdf_url":"https://academic.oup.com/nar/article-pdf/40/D1/D770/9482100/gkr874.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6000000238418579,"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322248","display_name":"Israel Academy of Sciences and Humanities","ror":"https://ror.org/03c6c9520"},{"id":"https://openalex.org/F4320323139","display_name":"Azrieli Foundation","ror":"https://ror.org/009svts64"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2116976883.pdf","grobid_xml":"https://content.openalex.org/works/W2116976883.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W49766303","https://openalex.org/W184330617","https://openalex.org/W399385914","https://openalex.org/W611231310","https://openalex.org/W1491459594","https://openalex.org/W1575273684","https://openalex.org/W1597762351","https://openalex.org/W1918334909","https://openalex.org/W1976548998","https://openalex.org/W1981673913","https://openalex.org/W1992306474","https://openalex.org/W2001916729","https://openalex.org/W2004235182","https://openalex.org/W2020916135","https://openalex.org/W2027243578","https://openalex.org/W2030712022","https://openalex.org/W2042067428","https://openalex.org/W2048214825","https://openalex.org/W2083527495","https://openalex.org/W2107409961","https://openalex.org/W2108229064","https://openalex.org/W2112951169","https://openalex.org/W2124193242","https://openalex.org/W2127916455","https://openalex.org/W2144010506","https://openalex.org/W2149202606","https://openalex.org/W2154126596","https://openalex.org/W2159482845","https://openalex.org/W2165612309","https://openalex.org/W2170427655","https://openalex.org/W2580150222","https://openalex.org/W3119605303","https://openalex.org/W4211082359","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2475866497","https://openalex.org/W1490606327","https://openalex.org/W2797548350","https://openalex.org/W4231071852","https://openalex.org/W2362078318","https://openalex.org/W220219137","https://openalex.org/W2561023381","https://openalex.org/W2316752057","https://openalex.org/W2348714797","https://openalex.org/W3081644756"],"abstract_inverted_index":{"The":[0,84,108],"laws":[1],"of":[2,7,66,69,93,96],"thermodynamics":[3],"constrain":[4],"the":[5,50,127],"action":[6],"biochemical":[8,14,70],"systems.":[9],"However,":[10],"thermodynamic":[11,31,67,115],"data":[12,117],"on":[13],"compounds":[15,71,97],"can":[16],"be":[17],"difficult":[18],"to":[19,24,87],"find":[20],"and":[21,63,72,77,81,98,105,113,130,132],"is":[22,38,111],"cumbersome":[23],"perform":[25],"calculations":[26],"with":[27,74],"manually.":[28],"Even":[29],"simple":[30,76],"questions":[32],"like":[33],"'how":[34],"much":[35],"Gibbs":[36,94],"energy":[37],"released":[39],"by":[40,49],"ATP":[41],"hydrolysis":[42],"at":[43],"pH":[44],"5?'":[45],"are":[46,118],"complicated":[47],"excessively":[48],"search":[51,80],"for":[52],"accurate":[53,64],"data.":[54],"To":[55],"address":[56],"this":[57],"problem,":[58],"eQuilibrator":[59,88,109],"couples":[60],"a":[61,75],"comprehensive":[62],"database":[65,128],"properties":[68],"reactions":[73,99],"powerful":[78],"online":[79],"calculation":[82,92],"interface.":[83],"web":[85],"interface":[86],"(http://equilibrator.weizmann.ac.il)":[89],"enables":[90],"easy":[91],"energies":[95],"given":[100],"arbitrary":[101],"pH,":[102],"ionic":[103],"strength":[104],"metabolite":[106],"concentrations.":[107],"code":[110],"open-source":[112],"all":[114],"source":[116],"freely":[119],"downloadable":[120],"in":[121],"standard":[122],"formats.":[123],"Here":[124],"we":[125],"describe":[126],"characteristics":[129],"implementation":[131],"demonstrate":[133],"its":[134],"use.":[135]},"counts_by_year":[{"year":2026,"cited_by_count":20},{"year":2025,"cited_by_count":28},{"year":2024,"cited_by_count":36},{"year":2023,"cited_by_count":52},{"year":2022,"cited_by_count":54},{"year":2021,"cited_by_count":80},{"year":2020,"cited_by_count":82},{"year":2019,"cited_by_count":50},{"year":2018,"cited_by_count":56},{"year":2017,"cited_by_count":53},{"year":2016,"cited_by_count":41},{"year":2015,"cited_by_count":23},{"year":2014,"cited_by_count":11},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":7}],"updated_date":"2026-06-27T08:28:00.272161","created_date":"2025-10-10T00:00:00"}
