{"id":"https://openalex.org/W4226381651","doi":"https://doi.org/10.1186/s13321-022-00604-9","title":"Surge: a fast open-source chemical graph generator","display_name":"Surge: a fast open-source chemical graph generator","publication_year":2022,"publication_date":"2022-04-23","ids":{"openalex":"https://openalex.org/W4226381651","doi":"https://doi.org/10.1186/s13321-022-00604-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/35461261"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-022-00604-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00604-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-022-00604-9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-022-00604-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014961672","display_name":"Brendan D. McKay","orcid":"https://orcid.org/0000-0002-3553-0496"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Brendan D. McKay","raw_affiliation_strings":["School of Computing, Australian National University, Canberra, ACT, 2601, Australia. brendan.mckay@anu.edu.au","School of Computing, Australian National University, Canberra, ACT, 2601, Australia"],"affiliations":[{"raw_affiliation_string":"School of Computing, Australian National University, Canberra, ACT, 2601, Australia. brendan.mckay@anu.edu.au","institution_ids":["https://openalex.org/I118347636"]},{"raw_affiliation_string":"School of Computing, Australian National University, Canberra, ACT, 2601, Australia","institution_ids":["https://openalex.org/I118347636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050147247","display_name":"Mehmet Aziz Yirik","orcid":"https://orcid.org/0000-0001-7520-7215"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Mehmet Aziz Yirik","raw_affiliation_strings":["Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743, Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743, Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040194803","display_name":"Christoph Steinbeck","orcid":"https://orcid.org/0000-0001-6966-0814"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christoph Steinbeck","raw_affiliation_strings":["Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743, Jena, Germany. christoph.steinbeck@uni-jena.de","Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743, Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743, Jena, Germany. christoph.steinbeck@uni-jena.de","institution_ids":["https://openalex.org/I76198965"]},{"raw_affiliation_string":"Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-University, Lessingstr. 8, 07743, Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014961672"],"corresponding_institution_ids":["https://openalex.org/I118347636"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1662,"currency":"EUR","value_usd":1792},"fwci":4.8276,"has_fulltext":true,"cited_by_count":37,"citation_normalized_percentile":{"value":0.95704517,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"14","issue":"1","first_page":"24","last_page":"24"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9911999702453613,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9815000295639038,"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":0.7129682898521423},{"id":"https://openalex.org/keywords/generator","display_name":"Generator (circuit theory)","score":0.6605789661407471},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.63703852891922},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.47267112135887146},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4445376992225647},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.43744656443595886},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.41204604506492615},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3413352370262146},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23059237003326416},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.1894168257713318},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14066213369369507},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.08912736177444458}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7129682898521423},{"id":"https://openalex.org/C2780992000","wikidata":"https://www.wikidata.org/wiki/Q17016113","display_name":"Generator (circuit theory)","level":3,"score":0.6605789661407471},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.63703852891922},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.47267112135887146},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4445376992225647},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.43744656443595886},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.41204604506492615},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3413352370262146},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23059237003326416},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.1894168257713318},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14066213369369507},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.08912736177444458},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-022-00604-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00604-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-022-00604-9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:35461261","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35461261","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:46ee11e4345d459eaf6280983a99bf6a","is_oa":true,"landing_page_url":"https://doaj.org/article/46ee11e4345d459eaf6280983a99bf6a","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 14, Iss 1, Pp 1-9 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9034616","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9034616","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-022-00604-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00604-9","pdf_url":"https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-022-00604-9","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.699999988079071,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309895","display_name":"Carl-Zeiss-Stiftung","ror":"https://ror.org/03ng4kg22"},{"id":"https://openalex.org/F4320313941","display_name":"Friedrich-Schiller-Universit\u00e4t Jena","ror":"https://ror.org/05qpz1x62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4226381651.pdf","grobid_xml":"https://content.openalex.org/works/W4226381651.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W567605243","https://openalex.org/W1970387238","https://openalex.org/W1975147762","https://openalex.org/W1981167315","https://openalex.org/W1986922777","https://openalex.org/W1988385430","https://openalex.org/W1990600049","https://openalex.org/W1999227640","https://openalex.org/W2013406992","https://openalex.org/W2046862405","https://openalex.org/W2050230275","https://openalex.org/W2098103160","https://openalex.org/W2114704115","https://openalex.org/W2153693853","https://openalex.org/W2160411185","https://openalex.org/W2406561743","https://openalex.org/W2433645443","https://openalex.org/W2519564115","https://openalex.org/W3097842688","https://openalex.org/W3102068512","https://openalex.org/W3118695441","https://openalex.org/W3120165387","https://openalex.org/W3160229201","https://openalex.org/W4253780382"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2011676020","https://openalex.org/W2329895846"],"abstract_inverted_index":{"Chemical":[0],"structure":[1,120],"generators":[2],"are":[3],"used":[4],"in":[5],"cheminformatics":[6],"to":[7,33,95],"produce":[8],"or":[9,36,53],"enumerate":[10],"virtual":[11],"molecules":[12],"based":[13,83],"on":[14,84],"a":[15,47,54,126],"set":[16,50,65],"of":[17,28,51,66,69,99,106],"boundary":[18],"conditions.":[19],"The":[20,42],"result":[21],"can":[22,45],"then":[23],"be":[24,46],"tested":[25],"for":[26,37],"properties":[27],"interest,":[29],"such":[30],"as":[31,40],"adherence":[32],"measured":[34],"data":[35],"their":[38],"suitability":[39],"drugs.":[41],"starting":[43],"point":[44],"potentially":[48],"fuzzy":[49],"fragments":[52],"molecular":[55],"formula.":[56,73],"In":[57],"the":[58,61,64,70,77,85,92,103,118],"latter":[59],"case,":[60],"generator":[62,81],"produces":[63],"constitutional":[67,79],"isomers":[68],"given":[71],"input":[72],"Here":[74],"we":[75],"present":[76,109],"novel":[78],"isomer":[80],"surge":[82,107,115],"canonical":[86],"generation":[87],"path":[88],"method.":[89],"Surge":[90,122],"uses":[91],"nauty":[93],"package":[94],"compute":[96],"automorphism":[97],"groups":[98],"graphs.":[100],"We":[101],"outline":[102],"working":[104],"principles":[105],"and":[108],"benchmarking":[110],"results":[111],"which":[112],"show":[113],"that":[114],"is":[116,123],"currently":[117],"fastest":[119],"generator.":[121],"available":[124],"under":[125],"liberal":[127],"open-source":[128],"license.":[129]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":2}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
