{"id":"https://openalex.org/W4317695442","doi":"https://doi.org/10.1186/s13321-022-00677-6","title":"Development of an open-source software for isomer enumeration","display_name":"Development of an open-source software for isomer enumeration","publication_year":2023,"publication_date":"2023-01-22","ids":{"openalex":"https://openalex.org/W4317695442","doi":"https://doi.org/10.1186/s13321-022-00677-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/36683047"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-022-00677-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00677-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00677-6","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","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00677-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042555338","display_name":"Salom\u00e9 R. Rieder","orcid":"https://orcid.org/0000-0001-8036-651X"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Salom\u00e9 R. Rieder","raw_affiliation_strings":["Laboratorium f\u00fcr Physikalische Chemie, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093, Z\u00fcrich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratorium f\u00fcr Physikalische Chemie, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071372647","display_name":"Marina P. Oliveira","orcid":"https://orcid.org/0000-0002-0216-9585"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Marina P. Oliveira","raw_affiliation_strings":["Laboratorium f\u00fcr Physikalische Chemie, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093, Z\u00fcrich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratorium f\u00fcr Physikalische Chemie, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019754904","display_name":"Sereina Riniker","orcid":"https://orcid.org/0000-0003-1893-4031"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Sereina Riniker","raw_affiliation_strings":["Laboratorium f\u00fcr Physikalische Chemie, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093, Z\u00fcrich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratorium f\u00fcr Physikalische Chemie, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005181934","display_name":"Philippe H. H\u00fcnenberger","orcid":"https://orcid.org/0000-0002-9420-7998"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Philippe H. H\u00fcnenberger","raw_affiliation_strings":["Laboratorium f\u00fcr Physikalische Chemie, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093, Z\u00fcrich, Switzerland. phil@igc.phys.chem.ethz.ch","Laboratorium f\u00fcr Physikalische Chemie, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093, Z\u00fcrich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Laboratorium f\u00fcr Physikalische Chemie, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093, Z\u00fcrich, Switzerland. phil@igc.phys.chem.ethz.ch","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Laboratorium f\u00fcr Physikalische Chemie, ETH Z\u00fcrich, Vladimir-Prelog-Weg 2, 8093, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5042555338"],"corresponding_institution_ids":["https://openalex.org/I35440088"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1456,"currency":"EUR","value_usd":1570},"fwci":1.0663,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.78314369,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"15","issue":"1","first_page":"10","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12292","display_name":"Graph Theory and Algorithms","score":0.9858999848365784,"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"}},"topics":[{"id":"https://openalex.org/T12292","display_name":"Graph Theory and Algorithms","score":0.9858999848365784,"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"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.982200026512146,"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":0.9818999767303467,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/enumeration","display_name":"Enumeration","score":0.9411935210227966},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6697853207588196},{"id":"https://openalex.org/keywords/open-source-software","display_name":"Open source software","score":0.6106382608413696},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5940647125244141},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5619164109230042},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.35885781049728394},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3282316327095032},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23679876327514648},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12193241715431213},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09008672833442688}],"concepts":[{"id":"https://openalex.org/C156340839","wikidata":"https://www.wikidata.org/wiki/Q2704791","display_name":"Enumeration","level":2,"score":0.9411935210227966},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6697853207588196},{"id":"https://openalex.org/C2988343187","wikidata":"https://www.wikidata.org/wiki/Q1130645","display_name":"Open source software","level":3,"score":0.6106382608413696},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5940647125244141},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5619164109230042},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.35885781049728394},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3282316327095032},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23679876327514648},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12193241715431213},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09008672833442688}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13321-022-00677-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00677-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00677-6","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:36683047","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36683047","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:pubmedcentral.nih.gov:9867865","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9867865","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9867865/pdf/13321_2022_Article_677.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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"},{"id":"pmh:oai:doaj.org/article:8bc94fdc8bd14aa49e597df6d1760fbe","is_oa":true,"landing_page_url":"https://doaj.org/article/8bc94fdc8bd14aa49e597df6d1760fbe","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 15, Iss 1, Pp 1-22 (2023)","raw_type":"article"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/597082","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/597082","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"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":"Journal of Cheminformatics, 15 (1)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000597082","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000597082","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/s13321-022-00677-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-022-00677-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-022-00677-6","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":[{"display_name":"Peace, Justice and strong institutions","score":0.6700000166893005,"id":"https://metadata.un.org/sdg/16"}],"awards":[{"id":"https://openalex.org/G1459315804","display_name":null,"funder_award_id":"200021-175944","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G2000326366","display_name":"A Combinatorial Computational Chemistry Approach to Force-Field Development","funder_award_id":"175944","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G4836148144","display_name":null,"funder_award_id":"20002","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G5256785375","display_name":null,"funder_award_id":"200021-","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G993971353","display_name":null,"funder_award_id":"200021","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320321652","display_name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich","ror":"https://ror.org/05a28rw58"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4317695442.pdf"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W606008011","https://openalex.org/W1517772841","https://openalex.org/W1535820104","https://openalex.org/W1585305433","https://openalex.org/W1975147762","https://openalex.org/W1986922777","https://openalex.org/W1990600049","https://openalex.org/W2038702914","https://openalex.org/W2044834685","https://openalex.org/W2049817705","https://openalex.org/W2074295485","https://openalex.org/W2075118281","https://openalex.org/W2104722869","https://openalex.org/W2111098766","https://openalex.org/W2114704115","https://openalex.org/W2124426186","https://openalex.org/W2126359798","https://openalex.org/W2147405597","https://openalex.org/W2158970513","https://openalex.org/W2170973067","https://openalex.org/W2405035126","https://openalex.org/W3081134496","https://openalex.org/W3107560796","https://openalex.org/W3120165387","https://openalex.org/W3151425441","https://openalex.org/W3160229201","https://openalex.org/W3189419457","https://openalex.org/W4226381651","https://openalex.org/W4230329868","https://openalex.org/W4254018170"],"related_works":["https://openalex.org/W4376877853","https://openalex.org/W1493891899","https://openalex.org/W4250928611","https://openalex.org/W4232280318","https://openalex.org/W166480398","https://openalex.org/W167327709","https://openalex.org/W4387839566","https://openalex.org/W4210922265","https://openalex.org/W4319870556","https://openalex.org/W2084742289"],"abstract_inverted_index":{"This":[0],"article":[1],"documents":[2],"enu,":[3],"a":[4,23,39,53],"freely-downloadable,":[5],"open-source":[6],"and":[7,20,100,110,116],"stand-alone":[8],"program":[9,27],"written":[10],"in":[11,77,86],"C++":[12],"for":[13,105],"the":[14,17,35,43,62,65,78,92,101],"enumeration":[15],"of":[16,22,38,45,52,64,68,80,91,95],"constitutional":[18,36,55],"isomers":[19,37],"stereoisomers":[21,51],"molecular":[24],"formula.":[25],"The":[26,50,71,89,108,122],"relies":[28],"on":[29,42,61,128],"graph":[30],"theory":[31],"to":[32],"enumerate":[33],"all":[34],"given":[40,54],"formula":[41],"basis":[44,63],"their":[46],"canonical":[47,81],"adjacency":[48],"matrix.":[49,70],"isomer":[56,72],"are":[57,114,120],"enumerated":[58],"as":[59],"well,":[60],"automorphism":[66],"group":[67],"this":[69],"list":[73],"is":[74,97,103,125],"then":[75],"reported":[76],"form":[79],"SMILES":[82],"strings":[83],"within":[84],"files":[85],"XML":[87],"format.":[88],"specification":[90],"molecule":[93],"family":[94],"interest":[96],"very":[98],"flexible":[99],"code":[102,124],"optimized":[104],"computational":[106],"efficiency.":[107],"algorithms":[109],"implementations":[111],"underlying":[112],"enu":[113,123],"described,":[115],"simple":[117],"illustrative":[118],"applications":[119],"presented.":[121],"freely":[126],"available":[127],"GitHub":[129],"at":[130],"https://github.com/csms-ethz/CombiFF":[131],".":[132]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}