{"id":"https://openalex.org/W2108021950","doi":"https://doi.org/10.1186/1758-2946-6-3","title":"Efficient ring perception for the Chemistry Development Kit","display_name":"Efficient ring perception for the Chemistry Development Kit","publication_year":2014,"publication_date":"2014-01-30","ids":{"openalex":"https://openalex.org/W2108021950","doi":"https://doi.org/10.1186/1758-2946-6-3","mag":"2108021950","pmid":"https://pubmed.ncbi.nlm.nih.gov/24479757"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-6-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-3","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/counter/pdf/10.1186/1758-2946-6-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005209468","display_name":"John W. May","orcid":null},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"John W May","raw_affiliation_strings":["Cheminformatics and Metabolism, European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. johnmay@ebi.ac.uk","Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cheminformatics and Metabolism, European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. johnmay@ebi.ac.uk","institution_ids":["https://openalex.org/I1303153112"]},{"raw_affiliation_string":"Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]},{"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/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I87048295","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christoph Steinbeck","raw_affiliation_strings":["Cheminformatics and Metabolism, European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK","Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cheminformatics and Metabolism, European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]},{"raw_affiliation_string":"Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5005209468"],"corresponding_institution_ids":["https://openalex.org/I1303153112","https://openalex.org/I87048295"],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":3.1419,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.92014482,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"6","issue":"1","first_page":"3","last_page":"3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.7279000282287598,"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":0.7279000282287598,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.10980000346899033,"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/T12527","display_name":"Chemistry and Stereochemistry Studies","score":0.041600000113248825,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7991776466369629},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6051468253135681},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.5606534481048584},{"id":"https://openalex.org/keywords/ring","display_name":"Ring (chemistry)","score":0.5482571125030518},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.47759342193603516},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.46626028418540955},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4630584418773651},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.43347904086112976},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3735925555229187},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.19367462396621704},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18366596102714539},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.13568115234375}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7991776466369629},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6051468253135681},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.5606534481048584},{"id":"https://openalex.org/C2780378348","wikidata":"https://www.wikidata.org/wiki/Q25351438","display_name":"Ring (chemistry)","level":2,"score":0.5482571125030518},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.47759342193603516},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.46626028418540955},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4630584418773651},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.43347904086112976},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3735925555229187},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.19367462396621704},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18366596102714539},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.13568115234375},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-6-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-3","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:24479757","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24479757","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:europepmc.org:2906087","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3922685","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-6-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-6-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-6-3","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":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.46000000834465027}],"awards":[{"id":"https://openalex.org/G8887556623","display_name":"BBSRC Industrial CASE Partnership Grant","funder_award_id":"BB/I532153/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2108021950.pdf","grobid_xml":"https://content.openalex.org/works/W2108021950.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1533819319","https://openalex.org/W1601495365","https://openalex.org/W1965680834","https://openalex.org/W1965998825","https://openalex.org/W1966878439","https://openalex.org/W1975147762","https://openalex.org/W1990451437","https://openalex.org/W1991615245","https://openalex.org/W2002055996","https://openalex.org/W2027482274","https://openalex.org/W2040524805","https://openalex.org/W2045873232","https://openalex.org/W2071056049","https://openalex.org/W2075307413","https://openalex.org/W2091223968","https://openalex.org/W2096541451","https://openalex.org/W2098889731","https://openalex.org/W2114720692","https://openalex.org/W2124426186","https://openalex.org/W2137608611","https://openalex.org/W2140611297","https://openalex.org/W2143000571","https://openalex.org/W2148797284","https://openalex.org/W2169678694","https://openalex.org/W2991918053","https://openalex.org/W3202268800"],"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/W3210319767","https://openalex.org/W132037564","https://openalex.org/W4246770172"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,32,48,94,119,185],"Chemistry":[2],"Development":[3],"Kit":[4],"(CDK)":[5],"is":[6,25,121,193,206],"an":[7,142],"open":[8,207],"source":[9,204,208],"Java":[10],"library":[11],"for":[12,53,81],"manipulating":[13],"and":[14,45,89,102,109,129,209],"processing":[15],"chemical":[16,23,30,83],"information.":[17],"A":[18],"key":[19],"aspect":[20],"in":[21,91,130,156,168],"handling":[22,82,151],"structures":[24],"the":[26,29,55,71,75,92,133,190,201],"determination":[27],"of":[28,34,57,64,74,100,105,144,152],"rings.":[31,106],"rings":[33,56,65,164,192],"a":[35,58,182,197],"structure":[36,59],"are":[37,112],"used":[38,68],"areas":[39,174],"including":[40],"descriptors,":[41],"stereochemistry,":[42],"similarity,":[43],"screening":[44],"atom":[46],"typing.":[47],"CDK":[49],"includes":[50],"multiple":[51],"algorithms":[52,80,95],"determining":[54],"on":[60,123],"demand.":[61],"Non-unique":[62],"descriptions":[63],"were":[66,136],"often":[67],"due":[69],"to":[70,138,165,188],"slower":[72],"performance":[73,120],"unique":[76,191],"alternatives.":[77],"RESULTS:":[78],"Efficient":[79],"ring":[84,177],"perception":[85,178],"have":[86,179],"been":[87],"implemented":[88],"optimised":[90],"CDK.":[93],"provide":[96],"much":[97,153],"faster":[98],"computation":[99,160],"new":[101,134],"existing":[103],"types":[104],"Several":[107,173],"optimisation":[108],"implementation":[110],"considerations":[111],"discussed":[113],"which":[114],"improve":[115],"real":[116],"case":[117],"usage.":[118],"measured":[122],"several":[124,131],"publicly":[125],"available":[126],"data":[127],"sets":[128],"cases":[132],"implementations":[135],"found":[137],"be":[139,166],"more":[140,162],"than":[141],"order":[143],"magnitude":[145],"faster.":[146],"CONCLUSIONS:":[147],"Algorithmic":[148],"improvements":[149],"allow":[150],"larger":[154],"datasets":[155],"reasonable":[157],"time.":[158],"Faster":[159],"allows":[161],"appropriate":[163],"utilised":[167],"procedures":[169],"such":[170],"as":[171],"aromaticity.":[172],"that":[175],"require":[176],"also":[180],"seen":[181],"noticeable":[183],"improvement.":[184],"time":[186],"taken":[187],"compute":[189],"now":[194],"comparable":[195],"allowing":[196],"correct":[198],"usage":[199],"throughout":[200],"toolkit.":[202],"All":[203],"code":[205],"freely":[210],"available.":[211]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
