{"id":"https://openalex.org/W7148333712","doi":"https://doi.org/10.1021/acs.jcim.5c03163","title":"EVODEX: A Cheminformatics Framework for Mechanistic Abstraction and Prediction of Enzymatic Reactions","display_name":"EVODEX: A Cheminformatics Framework for Mechanistic Abstraction and Prediction of Enzymatic Reactions","publication_year":2026,"publication_date":"2026-04-02","ids":{"openalex":"https://openalex.org/W7148333712","doi":"https://doi.org/10.1021/acs.jcim.5c03163","pmid":"https://pubmed.ncbi.nlm.nih.gov/41925163"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c03163","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c03163","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","pubmed"],"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/A5118623042","display_name":"Lais Lastre Conceicao","orcid":null},"institutions":[{"id":"https://openalex.org/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lais Lastre Conceicao","raw_affiliation_strings":["Department of Bioengineering","University of California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering","institution_ids":[]},{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5132764542","display_name":"Haohong Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haohong Lin","raw_affiliation_strings":["Department of Bioengineering","University of California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering","institution_ids":[]},{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5132768035","display_name":"Yu-Chieh Tai","orcid":null},"institutions":[{"id":"https://openalex.org/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu-Chieh Tai","raw_affiliation_strings":["Department of Bioengineering","University of California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering","institution_ids":[]},{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016947803","display_name":"Gongao Xue","orcid":null},"institutions":[{"id":"https://openalex.org/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gongao Xue","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences","University of California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences","institution_ids":[]},{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100399376","display_name":"Han Zhang","orcid":"https://orcid.org/0000-0003-3340-0433"},"institutions":[{"id":"https://openalex.org/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Han Zhang","raw_affiliation_strings":["Department of Bioengineering","University of California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering","institution_ids":[]},{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5132751516","display_name":"Chenyan Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chenyan Zhang","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences","University of California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences","institution_ids":[]},{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112099193","display_name":"J. Christopher Anderson","orcid":null},"institutions":[{"id":"https://openalex.org/I103922791","display_name":"QB3","ror":"https://ror.org/04n1n3n22","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I103922791","https://openalex.org/I180670191","https://openalex.org/I185103710","https://openalex.org/I95457486"]},{"id":"https://openalex.org/I2803209242","display_name":"University of California System","ror":"https://ror.org/00pjdza24","country_code":"US","type":"education","lineage":["https://openalex.org/I2803209242"]},{"id":"https://openalex.org/I4210095629","display_name":"Institute of Molecular Bioimaging and Physiology","ror":"https://ror.org/00s2j5046","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210095629","https://openalex.org/I4210155236"]}],"countries":["IT","US"],"is_corresponding":true,"raw_author_name":"J. Christopher Anderson","raw_affiliation_strings":["Berkeley National Laboratory, Molecular Biophysics and Integrated Bioimaging","Department of Bioengineering","QB3: California Institute for Quantitative Biological Research","University of California"],"raw_orcid":"https://orcid.org/0000-0002-9115-7323","affiliations":[{"raw_affiliation_string":"Berkeley National Laboratory, Molecular Biophysics and Integrated Bioimaging","institution_ids":["https://openalex.org/I4210095629"]},{"raw_affiliation_string":"Department of Bioengineering","institution_ids":[]},{"raw_affiliation_string":"QB3: California Institute for Quantitative Biological Research","institution_ids":["https://openalex.org/I103922791"]},{"raw_affiliation_string":"University of California","institution_ids":["https://openalex.org/I2803209242"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5112099193"],"corresponding_institution_ids":["https://openalex.org/I103922791","https://openalex.org/I2803209242","https://openalex.org/I4210095629"],"apc_list":null,"apc_paid":null,"fwci":8.5079,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.9773534,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"66","issue":"8","first_page":"4793","last_page":"4807"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.12210000306367874,"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":0.12210000306367874,"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":0.10750000178813934,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.09290000051259995,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.9538999795913696},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6687999963760376},{"id":"https://openalex.org/keywords/abstraction","display_name":"Abstraction","score":0.6200000047683716},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.5368000268936157},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5332000255584717},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.47290000319480896},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.4514999985694885}],"concepts":[{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.9538999795913696},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6687999963760376},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.6200000047683716},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5921000242233276},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5778999924659729},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5368000268936157},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5332000255584717},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.47290000319480896},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.4514999985694885},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4088999927043915},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.3968000113964081},{"id":"https://openalex.org/C90673727","wikidata":"https://www.wikidata.org/wiki/Q901718","display_name":"Product (mathematics)","level":2,"score":0.3628000020980835},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.32989999651908875},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3239000141620636},{"id":"https://openalex.org/C177801218","wikidata":"https://www.wikidata.org/wiki/Q36534","display_name":"Chemical reaction","level":2,"score":0.30970001220703125},{"id":"https://openalex.org/C69118441","wikidata":"https://www.wikidata.org/wiki/Q2941663","display_name":"Enzyme catalysis","level":3,"score":0.29429998993873596},{"id":"https://openalex.org/C2991944050","wikidata":"https://www.wikidata.org/wiki/Q36534","display_name":"Reaction conditions","level":3,"score":0.2822999954223633},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2671000063419342},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2639999985694885},{"id":"https://openalex.org/C203394866","wikidata":"https://www.wikidata.org/wiki/Q2881060","display_name":"Chemical database","level":2,"score":0.2597000002861023},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.2542000114917755}],"mesh":[{"descriptor_ui":"D000080911","descriptor_name":"Cheminformatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000080911","descriptor_name":"Cheminformatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c03163","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c03163","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":"pmid:41925163","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41925163","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1824085712","https://openalex.org/W1934481644","https://openalex.org/W2092471565","https://openalex.org/W2108723491","https://openalex.org/W2110235365","https://openalex.org/W2119866908","https://openalex.org/W2128601422","https://openalex.org/W2159628188","https://openalex.org/W2165612309","https://openalex.org/W2466795701","https://openalex.org/W2804515387","https://openalex.org/W2895341279","https://openalex.org/W2907470641","https://openalex.org/W2947423323","https://openalex.org/W2950955377","https://openalex.org/W3120686965","https://openalex.org/W3134564396","https://openalex.org/W3146384714","https://openalex.org/W3160706794","https://openalex.org/W3169183507","https://openalex.org/W4294216483","https://openalex.org/W4311481273","https://openalex.org/W4388917508","https://openalex.org/W4392752197","https://openalex.org/W4394680908","https://openalex.org/W4395065686","https://openalex.org/W4400943748","https://openalex.org/W4410497554","https://openalex.org/W4410542888","https://openalex.org/W4412672761","https://openalex.org/W4413331274","https://openalex.org/W4417153140"],"related_works":[],"abstract_inverted_index":{"EVODEX":[0,37,84],"is":[1,35,60],"a":[2,32,39,65,86],"cheminformatics":[3],"framework":[4],"for":[5,68],"reasoning":[6],"about":[7],"enzymatic":[8,20],"chemical":[9],"transformations.":[10],"It":[11],"represents":[12],"reactions":[13,21],"using":[14],"atom-mapped":[15],"structure":[16],"and":[17,48,98],"decomposes":[18],"multicomponent":[19],"into":[22],"mechanistically":[23,61],"meaningful":[24],"partial":[25],"transformations,":[26],"remaining":[27],"well-defined":[28],"even":[29],"when":[30,58],"only":[31,57],"single":[33],"reaction":[34,90,94],"known.":[36],"defines":[38],"hierarchy":[40],"of":[41,89,100],"abstractions":[42],"based":[43],"on":[44,75],"progressively":[45],"inclusive":[46],"\u03c3-bonded":[47],"\u03c0-conjugated":[49],"shells":[50],"around":[51],"reactive":[52],"centers,":[53],"retaining":[54],"electronic":[55],"context":[56],"it":[59],"required.":[62],"This":[63],"provides":[64],"deterministic":[66],"criterion":[67],"mechanistic":[69],"consistency":[70],"that":[71,92],"does":[72],"not":[73],"rely":[74],"curated":[76],"rules":[77],"or":[78],"statistical":[79],"generalization.":[80],"Applied":[81],"at":[82],"scale,":[83],"yields":[85],"compact":[87],"set":[88],"operators":[91],"support":[93],"validation,":[95],"product":[96],"enumeration,":[97],"interpretation":[99],"LC-MS":[101],"data.":[102]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2026-04-03T00:00:00"}