{"id":"https://openalex.org/W2205915548","doi":"https://doi.org/10.1021/ci600305h","title":"Molecular Query Language (MQL)A Context-Free Grammar for Substructure Matching","display_name":"Molecular Query Language (MQL)A Context-Free Grammar for Substructure Matching","publication_year":2007,"publication_date":"2007-01-11","ids":{"openalex":"https://openalex.org/W2205915548","doi":"https://doi.org/10.1021/ci600305h","mag":"2205915548","pmid":"https://pubmed.ncbi.nlm.nih.gov/17381167"},"language":"en","primary_location":{"id":"doi:10.1021/ci600305h","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci600305h","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/A5002124394","display_name":"Ewgenij Proschak","orcid":"https://orcid.org/0000-0003-1961-1859"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ewgenij Proschak","raw_affiliation_strings":["Johann Wolfgang Goethe-University, Institute of Organic Chemistry and Chemical Biology, Chair for Chem- and Bioinformatics, Siesmayerstr. 70, D-60323 Frankfurt am Main, Germany, and Tibotec BVBA, Generaal De Wittelaan L11 B3, 2800 Mechelen, Belgium"],"affiliations":[{"raw_affiliation_string":"Johann Wolfgang Goethe-University, Institute of Organic Chemistry and Chemical Biology, Chair for Chem- and Bioinformatics, Siesmayerstr. 70, D-60323 Frankfurt am Main, Germany, and Tibotec BVBA, Generaal De Wittelaan L11 B3, 2800 Mechelen, Belgium","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081681147","display_name":"J\u00f6rg K. Wegner","orcid":"https://orcid.org/0000-0002-1852-9434"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"J\u00f6rg K. Wegner","raw_affiliation_strings":["Johann Wolfgang Goethe-University, Institute of Organic Chemistry and Chemical Biology, Chair for Chem- and Bioinformatics, Siesmayerstr. 70, D-60323 Frankfurt am Main, Germany, and Tibotec BVBA, Generaal De Wittelaan L11 B3, 2800 Mechelen, Belgium"],"affiliations":[{"raw_affiliation_string":"Johann Wolfgang Goethe-University, Institute of Organic Chemistry and Chemical Biology, Chair for Chem- and Bioinformatics, Siesmayerstr. 70, D-60323 Frankfurt am Main, Germany, and Tibotec BVBA, Generaal De Wittelaan L11 B3, 2800 Mechelen, Belgium","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029269398","display_name":"Andreas Sch\u00fcller","orcid":"https://orcid.org/0000-0002-4443-4279"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Sch\u00fcller","raw_affiliation_strings":["Johann Wolfgang Goethe-University, Institute of Organic Chemistry and Chemical Biology, Chair for Chem- and Bioinformatics, Siesmayerstr. 70, D-60323 Frankfurt am Main, Germany, and Tibotec BVBA, Generaal De Wittelaan L11 B3, 2800 Mechelen, Belgium"],"affiliations":[{"raw_affiliation_string":"Johann Wolfgang Goethe-University, Institute of Organic Chemistry and Chemical Biology, Chair for Chem- and Bioinformatics, Siesmayerstr. 70, D-60323 Frankfurt am Main, Germany, and Tibotec BVBA, Generaal De Wittelaan L11 B3, 2800 Mechelen, Belgium","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028135456","display_name":"Gisbert Schneider","orcid":"https://orcid.org/0000-0001-6706-1084"},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Gisbert Schneider","raw_affiliation_strings":["Johann Wolfgang Goethe-University, Institute of Organic Chemistry and Chemical Biology, Chair for Chem- and Bioinformatics, Siesmayerstr. 70, D-60323 Frankfurt am Main, Germany, and Tibotec BVBA, Generaal De Wittelaan L11 B3, 2800 Mechelen, Belgium"],"affiliations":[{"raw_affiliation_string":"Johann Wolfgang Goethe-University, Institute of Organic Chemistry and Chemical Biology, Chair for Chem- and Bioinformatics, Siesmayerstr. 70, D-60323 Frankfurt am Main, Germany, and Tibotec BVBA, Generaal De Wittelaan L11 B3, 2800 Mechelen, Belgium","institution_ids":["https://openalex.org/I114090438"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036309068","display_name":"Uli Fechner","orcid":null},"institutions":[{"id":"https://openalex.org/I114090438","display_name":"Goethe University Frankfurt","ror":"https://ror.org/04cvxnb49","country_code":"DE","type":"education","lineage":["https://openalex.org/I114090438"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Uli Fechner","raw_affiliation_strings":["Johann Wolfgang Goethe-University, Institute of Organic Chemistry and Chemical Biology, Chair for Chem- and Bioinformatics, Siesmayerstr. 70, D-60323 Frankfurt am Main, Germany, and Tibotec BVBA, Generaal De Wittelaan L11 B3, 2800 Mechelen, Belgium"],"affiliations":[{"raw_affiliation_string":"Johann Wolfgang Goethe-University, Institute of Organic Chemistry and Chemical Biology, Chair for Chem- and Bioinformatics, Siesmayerstr. 70, D-60323 Frankfurt am Main, Germany, and Tibotec BVBA, Generaal De Wittelaan L11 B3, 2800 Mechelen, Belgium","institution_ids":["https://openalex.org/I114090438"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5002124394"],"corresponding_institution_ids":["https://openalex.org/I114090438"],"apc_list":null,"apc_paid":null,"fwci":3.3132,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.93446966,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"47","issue":"2","first_page":"295","last_page":"301"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9961000084877014,"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":0.9961000084877014,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.994700014591217,"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/T12292","display_name":"Graph Theory and Algorithms","score":0.9836999773979187,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8315802812576294},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.6940435171127319},{"id":"https://openalex.org/keywords/substructure","display_name":"Substructure","score":0.5245014429092407},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.5064681768417358},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5025832653045654},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5014078617095947},{"id":"https://openalex.org/keywords/abstract-syntax-tree","display_name":"Abstract syntax tree","score":0.4183545708656311},{"id":"https://openalex.org/keywords/subgraph-isomorphism-problem","display_name":"Subgraph isomorphism problem","score":0.4102880358695984},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3841598629951477},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.3025723993778229},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.2866257429122925},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1530255675315857}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8315802812576294},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6940435171127319},{"id":"https://openalex.org/C99679407","wikidata":"https://www.wikidata.org/wiki/Q56761637","display_name":"Substructure","level":2,"score":0.5245014429092407},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.5064681768417358},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5025832653045654},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5014078617095947},{"id":"https://openalex.org/C58646249","wikidata":"https://www.wikidata.org/wiki/Q127380","display_name":"Abstract syntax tree","level":3,"score":0.4183545708656311},{"id":"https://openalex.org/C131992880","wikidata":"https://www.wikidata.org/wiki/Q2528185","display_name":"Subgraph isomorphism problem","level":3,"score":0.4102880358695984},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3841598629951477},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3025723993778229},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.2866257429122925},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1530255675315857},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci600305h","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci600305h","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:17381167","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17381167","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":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.6700000166893005}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1977464943","https://openalex.org/W1998343450","https://openalex.org/W2002089154","https://openalex.org/W2007832879","https://openalex.org/W2008734993","https://openalex.org/W2018906911","https://openalex.org/W2022109349","https://openalex.org/W2041686943","https://openalex.org/W2060380565","https://openalex.org/W2086618639","https://openalex.org/W2116007667","https://openalex.org/W2126359798","https://openalex.org/W2143387021","https://openalex.org/W2143614763","https://openalex.org/W2215622313","https://openalex.org/W2498752956","https://openalex.org/W2554073607","https://openalex.org/W3081081509","https://openalex.org/W4240525777","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1573015311","https://openalex.org/W1570419641","https://openalex.org/W4386509167","https://openalex.org/W2889938001","https://openalex.org/W4293771607","https://openalex.org/W3165034028","https://openalex.org/W2296499206","https://openalex.org/W2153916713","https://openalex.org/W2023846184","https://openalex.org/W3210319767"],"abstract_inverted_index":{"We":[0,162],"have":[1],"developed":[2],"a":[3,23,58,86,118,139],"Java":[4,59,115],"library":[5],"for":[6,28,135,167],"substructure":[7],"matching":[8,69,133],"that":[9],"features":[10,53],"easy-to-read":[11],"syntax":[12],"and":[13,31,50],"extensibility.":[14],"This":[15],"molecular":[16],"query":[17],"language":[18],"(MQL)":[19],"is":[20,38],"grounded":[21],"on":[22],"context-free":[24],"grammar,":[25],"which":[26],"allows":[27],"straightforward":[29],"modification":[30],"extension.":[32],"The":[33,81],"formal":[34],"description":[35],"of":[36,77,110,138,153,158],"MQL":[37,98,122,154],"provided":[39],"in":[40],"this":[41],"paper.":[42],"Molecule":[43],"primitives":[44],"are":[45,64],"atoms,":[46],"bonds,":[47],"properties,":[48],"branching,":[49],"rings.":[51],"User-defined":[52],"can":[54],"be":[55],"added":[56],"via":[57],"interface.":[60],"In":[61],"MQL,":[62],"molecules":[63],"represented":[65],"as":[66],"graphs.":[67],"Substructure":[68],"was":[70,101],"implemented":[71,164],"using":[72],"the":[73,104,108,128,132,142,146,150,156,159,168],"Ullmann":[74,82],"algorithm":[75,83],"because":[76],"favorable":[78],"run-time":[79],"performance.":[80],"carries":[84],"out":[85],"fast":[87],"subgraph":[88],"isomorphism":[89],"search":[90],"by":[91,103],"combining":[92],"backtracking":[93],"with":[94],"effective":[95],"forward":[96],"checking.":[97],"software":[99],"design":[100],"driven":[102],"aim":[105],"to":[106,124,155],"facilitate":[107],"use":[109],"various":[111],"cheminformatics":[112],"toolkits.":[113],"Two":[114],"interfaces":[116,166],"provide":[117],"bridge":[119],"from":[120,149],"our":[121],"package":[123],"an":[125],"external":[126,160],"toolkit:":[127],"first":[129],"one":[130,144],"provides":[131],"rules":[134],"every":[136],"feature":[137],"particular":[140],"toolkit;":[141],"second":[143],"converts":[145],"found":[147],"match":[148],"internal":[151],"format":[152,157],"toolkit.":[161],"already":[163],"these":[165],"Chemistry":[169],"Development":[170],"Toolkit.":[171]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
