{"id":"https://openalex.org/W3090180360","doi":"https://doi.org/10.1007/s10822-020-00349-3","title":"DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology","display_name":"DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology","publication_year":2020,"publication_date":"2020-10-05","ids":{"openalex":"https://openalex.org/W3090180360","doi":"https://doi.org/10.1007/s10822-020-00349-3","mag":"3090180360","pmid":"https://pubmed.ncbi.nlm.nih.gov/33015739"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-020-00349-3","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-020-00349-3","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-020-00349-3.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10822-020-00349-3.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028419688","display_name":"Dimitar Yonchev","orcid":"https://orcid.org/0000-0001-5068-6424"},"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":false,"raw_author_name":"Dimitar Yonchev","raw_affiliation_strings":["Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universit\u00e4t, Endenicher Allee 19c, 53115, Bonn, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universit\u00e4t, Endenicher Allee 19c, 53115, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"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, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universit\u00e4t, Endenicher Allee 19c, 53115, Bonn, Germany. bajorath@bit.uni-bonn.de","Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universit\u00e4t, Endenicher Allee 19c, 53115, Bonn, Germany"],"raw_orcid":"https://orcid.org/0000-0002-0557-5714","affiliations":[{"raw_affiliation_string":"Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universit\u00e4t, Endenicher Allee 19c, 53115, Bonn, Germany. bajorath@bit.uni-bonn.de","institution_ids":["https://openalex.org/I135140700"]},{"raw_affiliation_string":"Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universit\u00e4t, Endenicher Allee 19c, 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":2890,"currency":"EUR","value_usd":3690},"apc_paid":{"value":2890,"currency":"EUR","value_usd":3690},"fwci":0.8743,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.80092593,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":"34","issue":"12","first_page":"1207","last_page":"1218"},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9984999895095825,"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/T11407","display_name":"Innovative Microfluidic and Catalytic Techniques Innovation","score":0.9921000003814697,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.613420844078064},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5589653849601746},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.42684227228164673},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4003129303455353},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.3235360383987427},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.2203013300895691},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07522791624069214}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.613420844078064},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5589653849601746},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.42684227228164673},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4003129303455353},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.3235360383987427},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.2203013300895691},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07522791624069214},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1007/s10822-020-00349-3","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-020-00349-3","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-020-00349-3.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:33015739","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33015739","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 computer-aided molecular design","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7595974","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7595974","pdf_url":null,"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 Comput Aided Mol Des","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1007/s10822-020-00349-3","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-020-00349-3","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-020-00349-3.pdf","source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Computer-Aided Molecular Design","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320311808","display_name":"J\u00fcrgen Manchot Stiftung","ror":null},{"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/W3090180360.pdf","grobid_xml":"https://content.openalex.org/works/W3090180360.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1981737096","https://openalex.org/W1988037271","https://openalex.org/W1991286793","https://openalex.org/W2008237205","https://openalex.org/W2017978384","https://openalex.org/W2034541070","https://openalex.org/W2034549041","https://openalex.org/W2037825667","https://openalex.org/W2053834050","https://openalex.org/W2069336305","https://openalex.org/W2081301924","https://openalex.org/W2081784419","https://openalex.org/W2096541451","https://openalex.org/W2101234009","https://openalex.org/W2119652738","https://openalex.org/W2127019019","https://openalex.org/W2132022337","https://openalex.org/W2156909104","https://openalex.org/W2160592148","https://openalex.org/W2163237834","https://openalex.org/W2297103558","https://openalex.org/W2322193123","https://openalex.org/W2389030099","https://openalex.org/W2401258374","https://openalex.org/W2578240541","https://openalex.org/W2749017887","https://openalex.org/W2787709708","https://openalex.org/W2805483395","https://openalex.org/W2899771611","https://openalex.org/W2901817218","https://openalex.org/W2902166068","https://openalex.org/W2911155903","https://openalex.org/W2925830236","https://openalex.org/W2949986955","https://openalex.org/W2962764565","https://openalex.org/W2979962592","https://openalex.org/W2989615256","https://openalex.org/W3000749537","https://openalex.org/W3015847087","https://openalex.org/W3094686696","https://openalex.org/W3104956673","https://openalex.org/W3193532674","https://openalex.org/W4210372362","https://openalex.org/W4230674625"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2380075625","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890"],"abstract_inverted_index":{"The":[0],"compound":[1,53],"optimization":[2,50,121],"monitor":[3],"(COMO)":[4],"approach":[5,12],"was":[6],"originally":[7],"developed":[8,46],"as":[9],"a":[10,69],"diagnostic":[11],"to":[13,47,80,92,107],"aid":[14],"in":[15,63],"evaluating":[16],"development":[17,127],"stages":[18],"of":[19,36,39,61,73,83,110,117,129],"analog":[20,31,40,88,112,131],"series":[21,41,89],"and":[22,42,52,67,102,115],"progress":[23],"made":[24],"during":[25],"lead":[26],"optimization.":[27],"COMO":[28,62,74],"uses":[29],"virtual":[30,118],"populations":[32],"for":[33,75,120],"the":[34,81,94,108,126],"assessment":[35],"chemical":[37,100],"saturation":[38,101],"has":[43],"been":[44],"further":[45],"bridge":[48],"between":[49],"diagnostics":[51,106],"design.":[54],"Herein,":[55],"we":[56],"discuss":[57],"key":[58],"methodological":[59],"features":[60],"its":[64],"scientific":[65],"context":[66],"present":[68],"deep":[70],"learning":[71],"extension":[72],"generative":[76],"molecular":[77],"design,":[78],"leading":[79],"introduction":[82],"DeepCOMO.":[84],"Applications":[85],"on":[86],"exemplary":[87],"are":[90],"reported":[91],"illustrate":[93],"entire":[95],"DeepCOMO":[96],"repertoire,":[97],"ranging":[98],"from":[99],"structure-activity":[103],"relationship":[104],"progression":[105],"evaluation":[109],"different":[111],"design":[113],"strategies":[114],"prioritization":[116],"candidates":[119],"efforts,":[122],"taking":[123],"into":[124],"account":[125],"stage":[128],"individual":[130],"series.":[132]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}