{"id":"https://openalex.org/W4410743308","doi":"https://doi.org/10.1186/s13321-025-01032-1","title":"Context-dependent similarity searching for small molecular fragments","display_name":"Context-dependent similarity searching for small molecular fragments","publication_year":2025,"publication_date":"2025-05-26","ids":{"openalex":"https://openalex.org/W4410743308","doi":"https://doi.org/10.1186/s13321-025-01032-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/40420123"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01032-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01032-1","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01032-1","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/s13321-025-01032-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007768420","display_name":"Atsushi Yoshimori","orcid":"https://orcid.org/0000-0003-3206-5143"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Atsushi Yoshimori","raw_affiliation_strings":["Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany","Institute for Theoretical Medicine, Inc., 26-1 Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa, 251-0012, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"Institute for Theoretical Medicine, Inc., 26-1 Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa, 251-0012, Japan","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039926688","display_name":"J\u00fcrgen Bajorath","orcid":"https://orcid.org/0000-0002-0557-5714"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J\u00fcrgen Bajorath","raw_affiliation_strings":["Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany. bajorath@bit.uni-bonn.de","Lamarr Institute for Machine Learning and Artificial Intelligence, University of Bonn, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany. bajorath@bit.uni-bonn.de"],"affiliations":[{"raw_affiliation_string":"Department of Life Science Informatics and Data Science, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, University of Bonn, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany. bajorath@bit.uni-bonn.de","institution_ids":[]},{"raw_affiliation_string":"Lamarr Institute for Machine Learning and Artificial Intelligence, University of Bonn, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany. bajorath@bit.uni-bonn.de","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5007768420"],"corresponding_institution_ids":["https://openalex.org/I135140700"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.12891628,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"1","first_page":"83","last_page":"83"},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.995199978351593,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9677000045776367,"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/cheminformatics","display_name":"Cheminformatics","score":0.8731825351715088},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.8668060302734375},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.742165207862854},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.659122109413147},{"id":"https://openalex.org/keywords/nearest-neighbor-search","display_name":"Nearest neighbor search","score":0.5832070708274841},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.5679712295532227},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.538283109664917},{"id":"https://openalex.org/keywords/word","display_name":"Word (group theory)","score":0.4670841693878174},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.46293821930885315},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.187588632106781},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.12189429998397827},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.068126380443573},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.06522810459136963}],"concepts":[{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.8731825351715088},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.8668060302734375},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.742165207862854},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.659122109413147},{"id":"https://openalex.org/C116738811","wikidata":"https://www.wikidata.org/wiki/Q608751","display_name":"Nearest neighbor search","level":2,"score":0.5832070708274841},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.5679712295532227},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.538283109664917},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.4670841693878174},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46293821930885315},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.187588632106781},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.12189429998397827},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.068126380443573},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.06522810459136963},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-01032-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01032-1","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01032-1","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:40420123","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40420123","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:66edbf06b4d94cdc975e6c290371445d","is_oa":true,"landing_page_url":"https://doaj.org/article/66edbf06b4d94cdc975e6c290371445d","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 17, Iss 1, Pp 1-11 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12107754","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12107754","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/s13321-025-01032-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01032-1","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01032-1","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":"Quality Education","score":0.5299999713897705,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320324900","display_name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn","ror":"https://ror.org/041nas322"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410743308.pdf","grobid_xml":"https://content.openalex.org/works/W4410743308.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1531510710","https://openalex.org/W1663984431","https://openalex.org/W1966109203","https://openalex.org/W1966613725","https://openalex.org/W1970240947","https://openalex.org/W1975147762","https://openalex.org/W2005518172","https://openalex.org/W2021720851","https://openalex.org/W2026265322","https://openalex.org/W2026910177","https://openalex.org/W2044834685","https://openalex.org/W2092712721","https://openalex.org/W2096541451","https://openalex.org/W2096729078","https://openalex.org/W2139731838","https://openalex.org/W2412446857","https://openalex.org/W2792455800","https://openalex.org/W2911155903","https://openalex.org/W3116869419","https://openalex.org/W4240773179","https://openalex.org/W4283311879","https://openalex.org/W4285992209","https://openalex.org/W4406382224"],"related_works":["https://openalex.org/W2558461359","https://openalex.org/W4292296636","https://openalex.org/W2747814245","https://openalex.org/W1963790256","https://openalex.org/W2090768198","https://openalex.org/W2089108696","https://openalex.org/W2074014730","https://openalex.org/W4206415530","https://openalex.org/W2383633458","https://openalex.org/W3194411068"],"abstract_inverted_index":{"Similarity":[0],"searching":[1,108,121],"is":[2,8,72,103,122],"a":[3,89,94,144,154],"mainstay":[4],"in":[5],"cheminformatics":[6],"that":[7,100],"generally":[9],"used":[10],"to":[11,37,57,92,105],"identify":[12],"compounds":[13],"with":[14],"desired":[15],"properties.":[16],"For":[17,157],"small":[18],"molecular":[19],"fragments,":[20],"similarity":[21,34,52,59,70,107,120,130,158],"calculations":[22],"based":[23,73],"on":[24,74,140],"standard":[25,116],"descriptors":[26],"often":[27],"have":[28,44],"limited":[29],"utility":[30],"for":[31,109,170],"establishing":[32,153],"meaningful":[33],"relationships":[35,60,131],"due":[36],"feature":[38],"sparseness.":[39],"As":[40],"an":[41],"alternative,":[42],"we":[43,98],"adapted":[45],"the":[46,113],"concept":[47],"of":[48,115,124,151],"context-depending":[49],"word":[50],"pair":[51],"from":[53],"natural":[54],"language":[55],"processing":[56],"evaluate":[58],"between":[61,132],"substituents":[62,110,142,152],"(R-groups)":[63],"taking":[64],"latent":[65],"characteristics":[66],"into":[67],"account.":[68],"Context-dependent":[69,119],"assessment":[71],"vector":[75],"embeddings":[76],"as":[77,88],"fragment":[78],"representations":[79],"generated":[80],"using":[81],"neural":[82],"networks.":[83],"With":[84],"active":[85],"analogue":[86],"series":[87],"model":[90],"system":[91],"establish":[93],"global":[95,145],"structure-activity":[96],"context,":[97],"demonstrate":[99],"this":[101],"approach":[102],"applicable":[104],"systematic":[106],"and":[111,127],"increases":[112],"performance":[114],"descriptor":[117],"representations.":[118],"capable":[123],"detecting":[125],"remote":[126],"functionally":[128],"relevant":[129],"substituents.":[133],"Alternative":[134],"search":[135],"queries":[136],"are":[137],"introduced":[138],"focusing":[139],"individual":[141,149],"within":[143],"substituent":[146],"context":[147],"or":[148,162],"sequences":[150],"local":[155],"context.":[156],"searching,":[159],"different":[160],"structural":[161],"structure-property":[163],"contexts":[164],"can":[165],"be":[166],"established,":[167],"providing":[168],"opportunities":[169],"various":[171],"applications.":[172]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}