{"id":"https://openalex.org/W1964189732","doi":"https://doi.org/10.1021/ci3002217","title":"Accurate Atom-Mapping Computation for Biochemical Reactions","display_name":"Accurate Atom-Mapping Computation for Biochemical Reactions","publication_year":2012,"publication_date":"2012-09-10","ids":{"openalex":"https://openalex.org/W1964189732","doi":"https://doi.org/10.1021/ci3002217","mag":"1964189732","pmid":"https://pubmed.ncbi.nlm.nih.gov/22963657"},"language":"en","primary_location":{"id":"doi:10.1021/ci3002217","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci3002217","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/A5053894822","display_name":"Mario Latendresse","orcid":"https://orcid.org/0000-0002-6292-0158"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mario Latendresse","raw_affiliation_strings":["SRI International,\r333 Ravenswood Ave., Menlo Park,\rCalifornia 94025, United States","SRI International,#R#333 Ravenswood Ave., Menlo Park,#R#California 94025, United States"],"affiliations":[{"raw_affiliation_string":"SRI International,\r333 Ravenswood Ave., Menlo Park,\rCalifornia 94025, United States","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"SRI International,#R#333 Ravenswood Ave., Menlo Park,#R#California 94025, United States","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067132470","display_name":"Jeremiah P. Malerich","orcid":null},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremiah P. Malerich","raw_affiliation_strings":["SRI International,\r333 Ravenswood Ave., Menlo Park,\rCalifornia 94025, United States","SRI International,#R#333 Ravenswood Ave., Menlo Park,#R#California 94025, United States"],"affiliations":[{"raw_affiliation_string":"SRI International,\r333 Ravenswood Ave., Menlo Park,\rCalifornia 94025, United States","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"SRI International,#R#333 Ravenswood Ave., Menlo Park,#R#California 94025, United States","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110573079","display_name":"Mike Travers","orcid":null},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mike Travers","raw_affiliation_strings":["SRI International,\r333 Ravenswood Ave., Menlo Park,\rCalifornia 94025, United States","SRI International,#R#333 Ravenswood Ave., Menlo Park,#R#California 94025, United States"],"affiliations":[{"raw_affiliation_string":"SRI International,\r333 Ravenswood Ave., Menlo Park,\rCalifornia 94025, United States","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"SRI International,#R#333 Ravenswood Ave., Menlo Park,#R#California 94025, United States","institution_ids":["https://openalex.org/I1298353152"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082071104","display_name":"Peter D. Karp","orcid":"https://orcid.org/0000-0002-5876-6418"},"institutions":[{"id":"https://openalex.org/I1298353152","display_name":"SRI International","ror":"https://ror.org/05s570m15","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1298353152"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter D. Karp","raw_affiliation_strings":["SRI International,\r333 Ravenswood Ave., Menlo Park,\rCalifornia 94025, United States","SRI International,#R#333 Ravenswood Ave., Menlo Park,#R#California 94025, United States"],"affiliations":[{"raw_affiliation_string":"SRI International,\r333 Ravenswood Ave., Menlo Park,\rCalifornia 94025, United States","institution_ids":["https://openalex.org/I1298353152"]},{"raw_affiliation_string":"SRI International,#R#333 Ravenswood Ave., Menlo Park,#R#California 94025, United States","institution_ids":["https://openalex.org/I1298353152"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5053894822"],"corresponding_institution_ids":["https://openalex.org/I1298353152"],"apc_list":null,"apc_paid":null,"fwci":2.758,"has_fulltext":false,"cited_by_count":81,"citation_normalized_percentile":{"value":0.90603278,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"52","issue":"11","first_page":"2970","last_page":"2982"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998000264167786,"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":0.9998000264167786,"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/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.9962000250816345,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9925000071525574,"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/atom","display_name":"Atom (system on chip)","score":0.7145957350730896},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5601158738136292},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5476109981536865},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5259813666343689},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3323802351951599}],"concepts":[{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.7145957350730896},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5601158738136292},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5476109981536865},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5259813666343689},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3323802351951599},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002244","descriptor_name":"Carbon","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013237","descriptor_name":"Stereoisomerism","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":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","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":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","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":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","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":true},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062126","descriptor_name":"Databases, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci3002217","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci3002217","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:22963657","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22963657","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":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1538191341","https://openalex.org/W1968971683","https://openalex.org/W1976672440","https://openalex.org/W1979537657","https://openalex.org/W1982870104","https://openalex.org/W1988391091","https://openalex.org/W1999619962","https://openalex.org/W2014328192","https://openalex.org/W2035429492","https://openalex.org/W2053040996","https://openalex.org/W2058880528","https://openalex.org/W2103708054","https://openalex.org/W2112855295","https://openalex.org/W2171986194","https://openalex.org/W4237293127"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","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/W2385191140"],"abstract_inverted_index":{"The":[0,122,242],"complete":[1],"atom":[2,80,113,135,190,205,209],"mapping":[3,28,104],"of":[4,11,23,29,37,58,71,78,82,103,141,163,170,183,211,217],"a":[5,9,62,72,83,108,138],"chemical":[6],"reaction":[7,85],"is":[8,32,124,198,231],"bijection":[10],"the":[12,16,21,56,69,79,101,116,164,171,184,195,212,232,237,249,255,262],"reactant":[13,25],"atoms":[14,18,60],"to":[15,51,129,207,240],"product":[17],"that":[19,65,194],"specifies":[20],"terminus":[22],"each":[24],"atom.":[26],"Atom":[27],"biochemical":[30,48,84,142],"reactions":[31,162],"useful":[33],"for":[34,42,55,111,137,167],"many":[35],"applications":[36],"systems":[38],"biology,":[39],"in":[40,68,176,248,253,267],"particular":[41],"metabolic":[43],"engineering":[44],"where":[45],"synthesizing":[46],"new":[47,109],"pathways":[49],"has":[50],"take":[52],"into":[53],"account":[54],"number":[57],"carbon":[59],"from":[61],"source":[63],"compound":[64],"are":[66],"conserved":[67],"synthesis":[70],"target":[73],"compound.":[74],"Rapid,":[75],"accurate":[76,234],"computation":[77],"mapping(s)":[81],"remains":[86],"elusive":[87],"despite":[88],"significant":[89],"work":[90],"on":[91,126,160],"this":[92,158],"topic.":[93],"In":[94],"particular,":[95],"past":[96],"researchers":[97],"did":[98],"not":[99],"validate":[100],"accuracy":[102],"algorithms.":[105],"We":[106,155,192],"introduce":[107],"method":[110],"computing":[112],"mappings":[114,136,206,210],"called":[115],"minimum":[117],"weighted":[118],"edit-distance":[119],"(MWED)":[120],"metric.":[121],"metric":[123],"based":[125],"bond":[127],"propensity":[128],"react":[130],"and":[131,219,235],"computes":[132],"biochemically":[133],"valid":[134],"large":[139],"percentage":[140],"reactions.":[143],"MWED":[144],"models":[145,172],"can":[146],"be":[147,174,246,259],"formulated":[148],"efficiently":[149],"as":[150],"Mixed-Integer":[151],"Linear":[152],"Programs":[153],"(MILPs).":[154],"have":[156],"demonstrated":[157],"approach":[159,230],"7501":[161],"MetaCyc":[165,250],"database":[166,251],"which":[168],"87%":[169],"could":[173],"solved":[175],"less":[177],"than":[178],"10":[179],"s.":[180],"For":[181],"2.1%":[182],"reactions,":[185],"we":[186],"found":[187],"multiple":[188],"optimal":[189],"mappings.":[191],"show":[193],"error":[196],"rate":[197],"0.9%":[199],"(22":[200],"reactions)":[201],"by":[202],"comparing":[203],"these":[204],"2446":[208],"manually":[213],"curated":[214],"Kyoto":[215],"Encyclopedia":[216],"Genes":[218],"Genomes":[220],"(KEGG)":[221],"RPAIR":[222],"database.":[223],"To":[224],"our":[225,227],"knowledge,":[226],"computational":[228],"atom-mapping":[229,243,256],"most":[233],"among":[236],"fastest":[238],"published":[239],"date.":[241],"data":[244],"will":[245,258],"available":[247,260],"later":[252,266],"2012;":[254],"software":[257,265],"within":[261],"Pathway":[263],"Tools":[264],"2012.":[268]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":9}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}