{"id":"https://openalex.org/W1999619962","doi":"https://doi.org/10.1021/ci200351b","title":"Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization","display_name":"Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization","publication_year":2011,"publication_date":"2011-11-19","ids":{"openalex":"https://openalex.org/W1999619962","doi":"https://doi.org/10.1021/ci200351b","mag":"1999619962","pmid":"https://pubmed.ncbi.nlm.nih.gov/22098204"},"language":"en","primary_location":{"id":"doi:10.1021/ci200351b","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200351b","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/A5002135830","display_name":"Eric L. First","orcid":null},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eric L. First","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048485981","display_name":"Chrysanthos E. Gounaris","orcid":"https://orcid.org/0000-0001-5779-2510"},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chrysanthos E. Gounaris","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States","institution_ids":["https://openalex.org/I20089843"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050187529","display_name":"Christodoulos A. Floudas","orcid":null},"institutions":[{"id":"https://openalex.org/I20089843","display_name":"Princeton University","ror":"https://ror.org/00hx57361","country_code":"US","type":"education","lineage":["https://openalex.org/I20089843"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christodoulos A. Floudas","raw_affiliation_strings":["Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States","institution_ids":["https://openalex.org/I20089843"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5002135830"],"corresponding_institution_ids":["https://openalex.org/I20089843"],"apc_list":null,"apc_paid":null,"fwci":4.0799,"has_fulltext":false,"cited_by_count":44,"citation_normalized_percentile":{"value":0.94035168,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"52","issue":"1","first_page":"84","last_page":"92"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer 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":0.9958999752998352,"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":0.9926999807357788,"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":0.6669225096702576},{"id":"https://openalex.org/keywords/integer","display_name":"Integer (computer science)","score":0.6057437062263489},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.46199989318847656},{"id":"https://openalex.org/keywords/integer-programming","display_name":"Integer programming","score":0.4520948529243469},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.44999682903289795},{"id":"https://openalex.org/keywords/linear-programming","display_name":"Linear programming","score":0.42190396785736084},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3728126883506775},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.06999242305755615}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6669225096702576},{"id":"https://openalex.org/C97137487","wikidata":"https://www.wikidata.org/wiki/Q729138","display_name":"Integer (computer science)","level":2,"score":0.6057437062263489},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.46199989318847656},{"id":"https://openalex.org/C56086750","wikidata":"https://www.wikidata.org/wiki/Q6042592","display_name":"Integer programming","level":2,"score":0.4520948529243469},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.44999682903289795},{"id":"https://openalex.org/C41045048","wikidata":"https://www.wikidata.org/wiki/Q202843","display_name":"Linear programming","level":2,"score":0.42190396785736084},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3728126883506775},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.06999242305755615},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","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":"D007700","descriptor_name":"Kinetics","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":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055601","descriptor_name":"Organic Chemistry Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055601","descriptor_name":"Organic Chemistry Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055601","descriptor_name":"Organic Chemistry Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci200351b","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200351b","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:22098204","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22098204","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/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320333566","display_name":"National Defense Science and Engineering Graduate","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1600402727","https://openalex.org/W1851431100","https://openalex.org/W1968971683","https://openalex.org/W1972641397","https://openalex.org/W1974032838","https://openalex.org/W1989875369","https://openalex.org/W1995714561","https://openalex.org/W1995860742","https://openalex.org/W2055677741","https://openalex.org/W2058880528","https://openalex.org/W2090486360","https://openalex.org/W2095132231","https://openalex.org/W2096725584","https://openalex.org/W2103626206","https://openalex.org/W2113221321","https://openalex.org/W2218035893","https://openalex.org/W4238484605"],"related_works":["https://openalex.org/W1925942709","https://openalex.org/W2047683846","https://openalex.org/W2044902158","https://openalex.org/W2983685817","https://openalex.org/W2082154838","https://openalex.org/W2109912052","https://openalex.org/W1711527768","https://openalex.org/W4285278887","https://openalex.org/W2995925505","https://openalex.org/W134783735"],"abstract_inverted_index":{"Reaction":[0],"mappings":[1,34,65,77,84],"are":[2],"of":[3,11,39,53,82,102,119],"fundamental":[4],"importance":[5],"to":[6,30,59,73,86,149],"researchers":[7],"studying":[8],"the":[9,37,51,106,120,138,150],"mechanisms":[10,89],"chemical":[12],"reactions":[13,122],"and":[14,79,110],"analyzing":[15],"biochemical":[16],"pathways.":[17],"We":[18,69,95],"have":[19],"developed":[20],"an":[21],"automated":[22],"method":[23,63],"based":[24],"on":[25,105],"integer":[26],"linear":[27],"optimization,":[28],"ILP,":[29],"identify":[31],"optimal":[32],"reaction":[33,76,88],"that":[35,49,66,117],"minimize":[36],"number":[38,52,101],"bond":[40,54],"changes.":[41,56],"An":[42],"alternate":[43],"objective":[44],"function":[45],"is":[46,146],"also":[47,70],"proposed":[48,132],"minimizes":[50],"order":[55],"In":[57],"contrast":[58],"previous":[60],"approaches,":[61],"our":[62,97],"produces":[64],"respect":[67],"stereochemistry.":[68],"show":[71],"how":[72],"locate":[74],"multiple":[75],"efficiently":[78],"determine":[80],"which":[81,145],"those":[83],"correspond":[85],"distinct":[87],"by":[90],"automatically":[91],"detecting":[92],"molecular":[93],"symmetries.":[94],"demonstrate":[96],"techniques":[98],"through":[99],"a":[100],"computational":[103,114],"studies":[104,115],"GRI-Mech,":[107],"KEGG":[108],"LIGAND,":[109],"BioPath":[111],"databases.":[112],"The":[113,131],"indicate":[116],"99%":[118],"8078":[121],"tested":[123],"can":[124],"be":[125],"addressed":[126],"within":[127],"1":[128],"CPU":[129],"hour.":[130],"framework":[133],"has":[134],"been":[135],"incorporated":[136],"into":[137],"Web":[139],"tool":[140],"DREAM":[141],"(":[142],"http://selene.princeton.edu/dream/":[143],"),":[144],"freely":[147],"available":[148],"scientific":[151],"community.":[152]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
