{"id":"https://openalex.org/W4406382224","doi":"https://doi.org/10.1186/s13321-025-00951-3","title":"Context-dependent similarity analysis of analogue series for structure\u2013activity relationship transfer based on a concept from natural language processing","display_name":"Context-dependent similarity analysis of analogue series for structure\u2013activity relationship transfer based on a concept from natural language processing","publication_year":2025,"publication_date":"2025-01-15","ids":{"openalex":"https://openalex.org/W4406382224","doi":"https://doi.org/10.1186/s13321-025-00951-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/39815340"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-00951-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00951-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00951-3","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/s13321-025-00951-3","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":[],"countries":[],"is_corresponding":false,"raw_author_name":"Atsushi Yoshimori","raw_affiliation_strings":["Institute for Theoretical Medicine, Inc., 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-0012, Japan"],"affiliations":[{"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":[{"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":"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","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","Lamarr Institute for Machine Learning and Artificial Intelligence, University of Bonn, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany"],"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":["https://openalex.org/I135140700"]},{"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":["https://openalex.org/I135140700"]},{"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":"Lamarr Institute for Machine Learning and Artificial Intelligence, University of Bonn, Friedrich-Hirzebruch-Allee 5/6, 53115, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5039926688"],"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":3.1375,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.89822804,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"17","issue":"1","first_page":"5","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9934999942779541,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9865999817848206,"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":0.8567709922790527},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.7619580030441284},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.7401561737060547},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7241992950439453},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.5567250847816467},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5208573937416077},{"id":"https://openalex.org/keywords/natural-language","display_name":"Natural language","score":0.5023086071014404},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.4911174476146698},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4348142147064209},{"id":"https://openalex.org/keywords/substituent","display_name":"Substituent","score":0.42157182097435},{"id":"https://openalex.org/keywords/word","display_name":"Word (group theory)","score":0.41098782420158386},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.4107043445110321},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.38563400506973267},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3659088611602783},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3358539640903473},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2203064262866974},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.150920569896698},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.13757964968681335},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.11781582236289978}],"concepts":[{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.8567709922790527},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.7619580030441284},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.7401561737060547},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7241992950439453},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.5567250847816467},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5208573937416077},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.5023086071014404},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.4911174476146698},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4348142147064209},{"id":"https://openalex.org/C2778689049","wikidata":"https://www.wikidata.org/wiki/Q898422","display_name":"Substituent","level":2,"score":0.42157182097435},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.41098782420158386},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.4107043445110321},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.38563400506973267},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3659088611602783},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3358539640903473},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2203064262866974},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.150920569896698},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.13757964968681335},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.11781582236289978},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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},{"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/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}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-00951-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00951-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00951-3","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:39815340","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39815340","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:11734349","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11734349","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11734349/pdf/13321_2025_Article_951.pdf","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"},{"id":"pmh:oai:doaj.org/article:164fe480377d4bec853914b3386b4936","is_oa":true,"landing_page_url":"https://doaj.org/article/164fe480377d4bec853914b3386b4936","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 1-14 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-00951-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00951-3","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00951-3","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":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.8199999928474426}],"awards":[],"funders":[{"id":"https://openalex.org/F4320324900","display_name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn","ror":"https://ror.org/041nas322"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4406382224.pdf"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1500036797","https://openalex.org/W1663984431","https://openalex.org/W1966109203","https://openalex.org/W1966613725","https://openalex.org/W1970240947","https://openalex.org/W1993187658","https://openalex.org/W2005518172","https://openalex.org/W2021137848","https://openalex.org/W2021720851","https://openalex.org/W2026265322","https://openalex.org/W2044834685","https://openalex.org/W2074231493","https://openalex.org/W2085313140","https://openalex.org/W2092712721","https://openalex.org/W2096541451","https://openalex.org/W2320534770","https://openalex.org/W2792455800","https://openalex.org/W2888349794","https://openalex.org/W2911155903","https://openalex.org/W2940024920","https://openalex.org/W2942782492","https://openalex.org/W3000409525","https://openalex.org/W3203279400","https://openalex.org/W4206478093","https://openalex.org/W4250830953","https://openalex.org/W4283311879","https://openalex.org/W4285992209"],"related_works":["https://openalex.org/W1573015311","https://openalex.org/W2889938001","https://openalex.org/W4386509167","https://openalex.org/W3165034028","https://openalex.org/W1570419641","https://openalex.org/W4293771607","https://openalex.org/W2296499206","https://openalex.org/W132037564","https://openalex.org/W3210319767","https://openalex.org/W2747814245"],"abstract_inverted_index":{"Analogue":[0],"series":[1,59,127],"(AS)":[2],"are":[3,12],"generated":[4],"during":[5],"compound":[6],"optimization":[7],"in":[8,103,147],"medicinal":[9,105],"chemistry":[10,106],"and":[11,31,92,107,124,155],"the":[13,40,134,137],"major":[14],"source":[15],"of":[16,22,26,111,139],"structure-activity":[17],"relationship":[18],"(SAR)":[19],"information.":[20],"Pairs":[21],"active":[23],"AS":[24,63,95],"consisting":[25],"compounds":[27],"with":[28,66,128],"corresponding":[29],"substituents":[30],"comparable":[32],"potency":[33],"progression":[34],"represent":[35],"SAR":[36,57,129],"transfer":[37,58,130],"events":[38],"for":[39,56,83,113,123,142],"same":[41],"target":[42],"or":[43],"across":[44],"different":[45],"targets.":[46],"We":[47],"report":[48],"a":[49,144],"new":[50,145],"computational":[51,104],"approach":[52,135],"to":[53,120,133],"systematically":[54,121],"search":[55,122],"that":[60],"combines":[61],"an":[62],"alignment":[64],"algorithm":[65],"context-depending":[67],"similarity":[68,98,141],"assessment":[69,99,138],"based":[70,151],"on":[71],"vector":[72,153],"embeddings":[73,154],"adapted":[74,159],"from":[75,160],"natural":[76,161],"language":[77,162],"processing.":[78,163],"The":[79],"methodology":[80],"comprehensively":[81],"accounts":[82],"substituent":[84],"similarity,":[85],"identifies":[86],"non-classical":[87],"bioisosteres,":[88],"captures":[89],"substituent-property":[90],"relationships,":[91],"generates":[93],"accurate":[94],"alignments.":[96],"Context-dependent":[97],"is":[100,118,136,150],"conceptually":[101],"novel":[102],"should":[108],"also":[109],"be":[110],"interest":[112],"other":[114],"applications.Scientific":[115],"contributionA":[116],"method":[117],"reported":[119],"align":[125],"analogue":[126],"potential.":[131],"Central":[132],"context-dependent":[140],"substituents,":[143],"concept":[146],"cheminformatics,":[148],"which":[149],"upon":[152],"word":[156],"pair":[157],"relationships":[158]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
