{"id":"https://openalex.org/W4308018181","doi":"https://doi.org/10.1021/acs.jcim.2c00426","title":"Representing Catalytic Mechanisms with Rule Composition","display_name":"Representing Catalytic Mechanisms with Rule Composition","publication_year":2022,"publication_date":"2022-11-03","ids":{"openalex":"https://openalex.org/W4308018181","doi":"https://doi.org/10.1021/acs.jcim.2c00426"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00426","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00426","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001028353","display_name":"Jakob L. Andersen","orcid":"https://orcid.org/0000-0002-4165-3732"},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Jakob L. Andersen","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark","institution_ids":["https://openalex.org/I177969490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021765002","display_name":"Rolf Fagerberg","orcid":"https://orcid.org/0000-0003-1004-3314"},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Rolf Fagerberg","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark","institution_ids":["https://openalex.org/I177969490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005564950","display_name":"Christoph Flamm","orcid":"https://orcid.org/0000-0001-5500-2415"},"institutions":[{"id":"https://openalex.org/I129774422","display_name":"University of Vienna","ror":"https://ror.org/03prydq77","country_code":"AT","type":"education","lineage":["https://openalex.org/I129774422"]}],"countries":["AT"],"is_corresponding":false,"raw_author_name":"Christoph Flamm","raw_affiliation_strings":["Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria"],"affiliations":[{"raw_affiliation_string":"Department of Theoretical Chemistry, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria","institution_ids":["https://openalex.org/I129774422"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067812040","display_name":"Walter Fontana","orcid":"https://orcid.org/0000-0003-4062-9957"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Walter Fontana","raw_affiliation_strings":["Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, United States"],"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, United States","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016152929","display_name":"Juraj Kol\u010d\u00e1k","orcid":"https://orcid.org/0000-0002-9407-9682"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["DK","US"],"is_corresponding":true,"raw_author_name":"Juri Kol\u010d\u00e1k","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark","Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, United States"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark","institution_ids":["https://openalex.org/I177969490"]},{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, United States","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042904279","display_name":"Christophe V. F. P. Laurent","orcid":"https://orcid.org/0000-0002-9112-6981"},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Christophe V.F.P. Laurent","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark","institution_ids":["https://openalex.org/I177969490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078883427","display_name":"Daniel Merkle","orcid":"https://orcid.org/0000-0001-7792-375X"},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["DK"],"is_corresponding":true,"raw_author_name":"Daniel Merkle","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark","institution_ids":["https://openalex.org/I177969490"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021113778","display_name":"Nikolai N\u00f8jgaard","orcid":"https://orcid.org/0000-0002-7053-4716"},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Nikolai N\u00f8jgaard","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark","institution_ids":["https://openalex.org/I177969490"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5016152929","https://openalex.org/A5078883427"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I177969490","https://openalex.org/I4210155419"],"apc_list":null,"apc_paid":null,"fwci":0.375,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.50752597,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"62","issue":"22","first_page":"5513","last_page":"5524"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9243999719619751,"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"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9243999719619751,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/composition","display_name":"Composition (language)","score":0.6087755560874939},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41580620408058167},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.09425792098045349}],"concepts":[{"id":"https://openalex.org/C40231798","wikidata":"https://www.wikidata.org/wiki/Q1333743","display_name":"Composition (language)","level":2,"score":0.6087755560874939},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41580620408058167},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.09425792098045349},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c00426","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00426","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmh:oai:sdu.dk:openaire_cris_publications/f29119c5-3edb-43d9-8a46-b189ebb96512","is_oa":false,"landing_page_url":"https://portal.findresearcher.sdu.dk/da/publications/f29119c5-3edb-43d9-8a46-b189ebb96512","pdf_url":null,"source":{"id":"https://openalex.org/S4306400423","display_name":"University of Southern Denmark Research Portal (University of Southern Denmark)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177969490","host_organization_name":"University of Southern Denmark","host_organization_lineage":["https://openalex.org/I177969490"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Andersen, J L, Fagerberg, R, Flamm, C, Fontana, W, Kol\u010d\u00e1k, J, Laurent, C V F P, Merkle, D & N\u00f8jgaard, N 2022, 'Representing catalytic mechanisms with rule composition', Journal of Chemical Information and Modeling, vol. 62, no. 22, pp. 5513-5524. https://doi.org/10.1021/acs.jcim.2c00426","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1032663478","display_name":null,"funder_award_id":"NNF19OC0057834","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G3220907668","display_name":null,"funder_award_id":"DFF-0135-00420B","funder_id":"https://openalex.org/F4320322928","funder_display_name":"Danmarks Frie Forskningsfond"},{"id":"https://openalex.org/G3843702472","display_name":null,"funder_award_id":"NNF21OC0066551","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G7176244305","display_name":null,"funder_award_id":"DFF-7014-00041","funder_id":"https://openalex.org/F4320322928","funder_display_name":"Danmarks Frie Forskningsfond"}],"funders":[{"id":"https://openalex.org/F4320322928","display_name":"Danmarks Frie Forskningsfond","ror":"https://ror.org/02sptwz63"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1983823113","https://openalex.org/W2033788780","https://openalex.org/W2041220366","https://openalex.org/W2164661513","https://openalex.org/W2765284721","https://openalex.org/W2772491215","https://openalex.org/W2895689867","https://openalex.org/W2918364177","https://openalex.org/W2991423243","https://openalex.org/W3112376646","https://openalex.org/W3147781287","https://openalex.org/W3182883085","https://openalex.org/W3184630098"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"An":[0],"\u201cimaginary":[1],"transition":[2,62,65],"structure\u201d":[3],"overlays":[4],"the":[5,9,25,77,95,100,128,132],"molecular":[6],"graphs":[7],"of":[8,14,89,102,119],"educt":[10],"and":[11,59,80,107,109],"product":[12],"sides":[13],"an":[15,55,86],"elementary":[16],"chemical":[17],"reaction":[18],"in":[19,27,39,113],"a":[20,40,60,114],"single":[21],"graph":[22],"to":[23,34,53,97,111],"highlight":[24],"changes":[26,72],"bond":[28,71],"structure.":[29,63],"We":[30,93],"generalize":[31],"this":[32],"idea":[33],"reactions":[35,118],"with":[36,127],"complex":[37],"mechanisms":[38,123],"formally":[41],"rigorous":[42],"approach":[43],"based":[44],"on":[45],"composing":[46],"arrow-pushing":[47],"steps":[48],"represented":[49],"as":[50],"graph-transformation":[51],"rules":[52],"construct":[54],"overall":[56,78],"composite":[57,134],"rule":[58],"derived":[61],"This":[64],"structure":[66],"retains":[67],"information":[68],"about":[69],"transient":[70],"that":[73,124],"are":[74,125],"invisible":[75],"at":[76],"level":[79],"can":[81],"be":[82],"constructed":[83,133],"automatically":[84],"from":[85],"existing":[87],"database":[88,116],"detailed":[90],"enzymatic":[91],"mechanisms.":[92],"use":[94],"construction":[96],"(i)":[98],"illuminate":[99],"distribution":[101],"catalytic":[103],"action":[104],"across":[105],"enzymes":[106],"substrates":[108],"(ii)":[110],"search":[112],"large":[115],"for":[117],"known":[120],"or":[121],"unknown":[122],"compatible":[126],"mechanism":[129],"captured":[130],"by":[131],"rule.":[135]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
