{"id":"https://openalex.org/W2047708582","doi":"https://doi.org/10.1021/ci2005548","title":"Drug Side-Effect Prediction Based on the Integration of Chemical and Biological Spaces","display_name":"Drug Side-Effect Prediction Based on the Integration of Chemical and Biological Spaces","publication_year":2012,"publication_date":"2012-11-17","ids":{"openalex":"https://openalex.org/W2047708582","doi":"https://doi.org/10.1021/ci2005548","mag":"2047708582","pmid":"https://pubmed.ncbi.nlm.nih.gov/23157436"},"language":"en","primary_location":{"id":"doi:10.1021/ci2005548","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci2005548","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035394108","display_name":"Yoshihiro Yamanishi","orcid":"https://orcid.org/0000-0003-2279-8773"},"institutions":[{"id":"https://openalex.org/I135598925","display_name":"Kyushu University","ror":"https://ror.org/00p4k0j84","country_code":"JP","type":"education","lineage":["https://openalex.org/I135598925"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yoshihiro Yamanishi","raw_affiliation_strings":["Division of System Cohort, Multi-scale Research Center for Medical Science, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan"],"affiliations":[{"raw_affiliation_string":"Division of System Cohort, Multi-scale Research Center for Medical Science, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan","institution_ids":["https://openalex.org/I135598925"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067908150","display_name":"Edouard Pauwels","orcid":"https://orcid.org/0000-0002-8180-075X"},"institutions":[{"id":"https://openalex.org/I70768539","display_name":"\u00c9cole Nationale Sup\u00e9rieure des Mines de Paris","ror":"https://ror.org/04y8cs423","country_code":"FR","type":"education","lineage":["https://openalex.org/I190752583","https://openalex.org/I2746051580","https://openalex.org/I70768539"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"funder","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I80043","display_name":"Institut Curie","ror":"https://ror.org/04t0gwh46","country_code":"FR","type":"funder","lineage":["https://openalex.org/I80043"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Edouard Pauwels","raw_affiliation_strings":["INSERM U900, F-75248, Paris, France","Institut Curie, F-75248, Paris, France","Mines ParisTech, Centre for Computational Biology, 35 rue Saint-Honore, F-77305 Fontainebleau Cedex, France","Mines ParisTech, Centre for Computational#R#Biology, 35 rue Saint-Honore, F-77305#R#Fontainebleau Cedex, France"],"affiliations":[{"raw_affiliation_string":"INSERM U900, F-75248, Paris, France","institution_ids":["https://openalex.org/I154526488"]},{"raw_affiliation_string":"Institut Curie, F-75248, Paris, France","institution_ids":["https://openalex.org/I80043"]},{"raw_affiliation_string":"Mines ParisTech, Centre for Computational Biology, 35 rue Saint-Honore, F-77305 Fontainebleau Cedex, France","institution_ids":["https://openalex.org/I70768539"]},{"raw_affiliation_string":"Mines ParisTech, Centre for Computational#R#Biology, 35 rue Saint-Honore, F-77305#R#Fontainebleau Cedex, France","institution_ids":["https://openalex.org/I70768539"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058370326","display_name":"Masaaki Kotera","orcid":"https://orcid.org/0000-0001-8188-3623"},"institutions":[{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masaaki Kotera","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan","Bioinformatics Center, Institute\rfor Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"raw_affiliation_string":"Bioinformatics Center, Institute\rfor Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5035394108"],"corresponding_institution_ids":["https://openalex.org/I135598925"],"apc_list":null,"apc_paid":null,"fwci":8.9839,"has_fulltext":false,"cited_by_count":146,"citation_normalized_percentile":{"value":0.98399367,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"52","issue":"12","first_page":"3284","last_page":"3292"},"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9916999936103821,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11460","display_name":"Analytical Methods in Pharmaceuticals","score":0.9764000177383423,"subfield":{"id":"https://openalex.org/subfields/1602","display_name":"Analytical 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/drugbank","display_name":"DrugBank","score":0.8662939071655273},{"id":"https://openalex.org/keywords/chemical-space","display_name":"Chemical space","score":0.6823620796203613},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.657101035118103},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4915834367275238},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.4905053973197937},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4740809202194214},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.44548171758651733},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4258810877799988},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.41913822293281555},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.3489707112312317},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34106171131134033},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33767643570899963},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.25723522901535034},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23203271627426147},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.23099905252456665},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20119652152061462},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1705302596092224},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.15383806824684143},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11463722586631775}],"concepts":[{"id":"https://openalex.org/C155261790","wikidata":"https://www.wikidata.org/wiki/Q1122544","display_name":"DrugBank","level":3,"score":0.8662939071655273},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.6823620796203613},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.657101035118103},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4915834367275238},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.4905053973197937},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4740809202194214},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.44548171758651733},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4258810877799988},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.41913822293281555},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.3489707112312317},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34106171131134033},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33767643570899963},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.25723522901535034},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23203271627426147},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.23099905252456665},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20119652152061462},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1705302596092224},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.15383806824684143},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11463722586631775},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci2005548","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci2005548","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:23157436","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23157436","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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:HAL:hal-03954127v1","is_oa":false,"landing_page_url":"https://hal.science/hal-03954127","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://pubs.acs.org/doi/10.1021/ci2005548","raw_type":"Journal articles"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.800000011920929,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1542652324","https://openalex.org/W1971387816","https://openalex.org/W1976526581","https://openalex.org/W1979845492","https://openalex.org/W1997453506","https://openalex.org/W2001515828","https://openalex.org/W2001565801","https://openalex.org/W2009313526","https://openalex.org/W2025341678","https://openalex.org/W2044542784","https://openalex.org/W2048435239","https://openalex.org/W2049454409","https://openalex.org/W2049946556","https://openalex.org/W2053080554","https://openalex.org/W2074192927","https://openalex.org/W2100672820","https://openalex.org/W2104950117","https://openalex.org/W2108069034","https://openalex.org/W2139516171","https://openalex.org/W2139736926","https://openalex.org/W2142572836","https://openalex.org/W2151241390","https://openalex.org/W2153838454","https://openalex.org/W2154896031","https://openalex.org/W2162422091","https://openalex.org/W2216412596","https://openalex.org/W2418844003","https://openalex.org/W4211208250"],"related_works":["https://openalex.org/W4382246684","https://openalex.org/W4387845407","https://openalex.org/W2902857455","https://openalex.org/W4207004502","https://openalex.org/W2151971404","https://openalex.org/W4212982662","https://openalex.org/W2160244398","https://openalex.org/W2907885506","https://openalex.org/W2022444336","https://openalex.org/W4385760073"],"abstract_inverted_index":{"Drug":[0],"side-effects,":[1],"or":[2],"adverse":[3],"drug":[4,21,25,58,102,110,176,202],"reactions,":[5],"have":[6,29],"become":[7],"a":[8,41,49,71,114,118,170],"major":[9],"public":[10],"health":[11],"concern":[12],"and":[13,23,66,105,142,146,160,164,181],"remain":[14],"one":[15],"of":[16,20,24,36,57,78,97,101,109,124,132,162,200],"the":[17,31,34,95,98,106,122,125,129,149,156,201],"main":[18],"causes":[19],"failure":[22],"withdrawal":[26],"once":[27],"they":[28],"reached":[30],"market.":[32],"Therefore,":[33],"identification":[35],"potential":[37,54],"severe":[38],"side-effects":[39,134],"is":[40,192],"challenging":[42],"issue.":[43],"In":[44],"this":[45],"paper,":[46],"we":[47,120],"develop":[48],"new":[50],"method":[51,127,191],"to":[52,85,155,194],"predict":[53],"side-effect":[55,172],"profiles":[56,145],"candidate":[59],"molecules":[60,177],"based":[61],"on":[62,70,128],"their":[63,139],"chemical":[64,99,103,140,163],"structures":[65,104],"target":[67,111,143],"protein":[68,144],"information":[69,187],"large":[72],"scale.":[73],"We":[74,167],"propose":[75],"several":[76],"extensions":[77],"kernel":[79],"regression":[80,158],"model":[81,159],"for":[82,135,174],"multiple":[83],"responses":[84],"deal":[86],"with":[87],"heterogeneous":[88],"data":[89],"sources.":[90,188],"The":[91,189],"originality":[92],"lies":[93],"in":[94,113,179],"integration":[96,161],"space":[100,108],"biological":[107,165],"proteins":[112],"unified":[115],"framework.":[116],"As":[117],"result,":[119],"demonstrate":[121],"usefulness":[123],"proposed":[126,157,190],"simultaneous":[130],"prediction":[131,150,173],"969":[133],"approved":[136],"drugs":[137],"from":[138],"substructure":[141],"show":[147],"that":[148],"accuracy":[151],"consistently":[152],"improves":[153],"owing":[154],"information.":[166],"also":[168],"conduct":[169],"comprehensive":[171],"uncharacterized":[175],"stored":[178],"DrugBank":[180],"confirm":[182],"interesting":[183],"predictions":[184],"using":[185],"independent":[186],"expected":[193],"be":[195],"useful":[196],"at":[197],"many":[198],"stages":[199],"development":[203],"process.":[204]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":19},{"year":2018,"cited_by_count":15},{"year":2017,"cited_by_count":15},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":6}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
