{"id":"https://openalex.org/W3179318616","doi":"https://doi.org/10.1093/bioinformatics/btab301","title":"Optimizing blood\u2013brain barrier permeation through deep reinforcement learning for <i>de novo</i> drug design","display_name":"Optimizing blood\u2013brain barrier permeation through deep reinforcement learning for <i>de novo</i> drug design","publication_year":2021,"publication_date":"2021-06-07","ids":{"openalex":"https://openalex.org/W3179318616","doi":"https://doi.org/10.1093/bioinformatics/btab301","mag":"3179318616","pmid":"https://pubmed.ncbi.nlm.nih.gov/34252946"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab301","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab301","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i84/39620366/btab301.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i84/39620366/btab301.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020082077","display_name":"Tiago Pereira","orcid":"https://orcid.org/0000-0003-2487-0097"},"institutions":[{"id":"https://openalex.org/I60858718","display_name":"University of Aveiro","ror":"https://ror.org/00nt41z93","country_code":"PT","type":"education","lineage":["https://openalex.org/I60858718"]},{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Tiago Pereira","raw_affiliation_strings":["CSUC/DEI, University of Coimbra , Coimbra 3030-290, Portugal","IEETA/DETI, University of Aveiro , Aveiro 3810-193, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CSUC/DEI, University of Coimbra , Coimbra 3030-290, Portugal","institution_ids":["https://openalex.org/I76903346"]},{"raw_affiliation_string":"IEETA/DETI, University of Aveiro , Aveiro 3810-193, Portugal","institution_ids":["https://openalex.org/I60858718"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064251517","display_name":"Maryam Abbasi","orcid":"https://orcid.org/0000-0002-9011-0734"},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Maryam Abbasi","raw_affiliation_strings":["CSUC/DEI, University of Coimbra , Coimbra 3030-290, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CSUC/DEI, University of Coimbra , Coimbra 3030-290, Portugal","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040524956","display_name":"Jos\u00e9 Lu\u00eds Oliveira","orcid":"https://orcid.org/0000-0002-6672-6176"},"institutions":[{"id":"https://openalex.org/I60858718","display_name":"University of Aveiro","ror":"https://ror.org/00nt41z93","country_code":"PT","type":"education","lineage":["https://openalex.org/I60858718"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Luis Oliveira","raw_affiliation_strings":["IEETA/DETI, University of Aveiro , Aveiro 3810-193, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IEETA/DETI, University of Aveiro , Aveiro 3810-193, Portugal","institution_ids":["https://openalex.org/I60858718"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046882659","display_name":"Bernardete Ribeiro","orcid":"https://orcid.org/0000-0002-9770-7672"},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Bernardete Ribeiro","raw_affiliation_strings":["CSUC/DEI, University of Coimbra , Coimbra 3030-290, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CSUC/DEI, University of Coimbra , Coimbra 3030-290, Portugal","institution_ids":["https://openalex.org/I76903346"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043572862","display_name":"Joel P. Arrais","orcid":"https://orcid.org/0000-0003-4937-2334"},"institutions":[{"id":"https://openalex.org/I76903346","display_name":"University of Coimbra","ror":"https://ror.org/04z8k9a98","country_code":"PT","type":"education","lineage":["https://openalex.org/I76903346"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Joel Arrais","raw_affiliation_strings":["CSUC/DEI, University of Coimbra , Coimbra 3030-290, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CSUC/DEI, University of Coimbra , Coimbra 3030-290, Portugal","institution_ids":["https://openalex.org/I76903346"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5020082077"],"corresponding_institution_ids":["https://openalex.org/I60858718","https://openalex.org/I76903346"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.629,"has_fulltext":false,"cited_by_count":26,"citation_normalized_percentile":{"value":0.88644689,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"37","issue":"Supplement_1","first_page":"i84","last_page":"i92"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11193","display_name":"Adenosine and Purinergic Signaling","score":0.3725999891757965,"subfield":{"id":"https://openalex.org/subfields/1314","display_name":"Physiology"},"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"}},"topics":[{"id":"https://openalex.org/T11193","display_name":"Adenosine and Purinergic Signaling","score":0.3725999891757965,"subfield":{"id":"https://openalex.org/subfields/1314","display_name":"Physiology"},"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"}},{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.2964000105857849,"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"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.17219999432563782,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/reinforcement-learning","display_name":"Reinforcement learning","score":0.7145494222640991},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6500449776649475},{"id":"https://openalex.org/keywords/bespoke","display_name":"Bespoke","score":0.6053892374038696},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4607990086078644},{"id":"https://openalex.org/keywords/generator","display_name":"Generator (circuit theory)","score":0.4573925733566284},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45061835646629333},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.3349915146827698},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12367454171180725}],"concepts":[{"id":"https://openalex.org/C97541855","wikidata":"https://www.wikidata.org/wiki/Q830687","display_name":"Reinforcement learning","level":2,"score":0.7145494222640991},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6500449776649475},{"id":"https://openalex.org/C44210515","wikidata":"https://www.wikidata.org/wiki/Q16968978","display_name":"Bespoke","level":2,"score":0.6053892374038696},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4607990086078644},{"id":"https://openalex.org/C2780992000","wikidata":"https://www.wikidata.org/wiki/Q17016113","display_name":"Generator (circuit theory)","level":3,"score":0.4573925733566284},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45061835646629333},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.3349915146827698},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12367454171180725},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001692","descriptor_name":"Biological Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001692","descriptor_name":"Biological Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001692","descriptor_name":"Biological Transport","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001812","descriptor_name":"Blood-Brain Barrier","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001812","descriptor_name":"Blood-Brain Barrier","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001812","descriptor_name":"Blood-Brain Barrier","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab301","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab301","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i84/39620366/btab301.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34252946","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34252946","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:8336597","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8336597","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab301","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab301","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/Supplement_1/i84/39620366/btab301.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1500036797","https://openalex.org/W1723097356","https://openalex.org/W1757990252","https://openalex.org/W1975391500","https://openalex.org/W1981276685","https://openalex.org/W1988037271","https://openalex.org/W1993966269","https://openalex.org/W2009315806","https://openalex.org/W2025281001","https://openalex.org/W2027478081","https://openalex.org/W2034549041","https://openalex.org/W2060846151","https://openalex.org/W2119717200","https://openalex.org/W2121863487","https://openalex.org/W2160592148","https://openalex.org/W2171639300","https://openalex.org/W2398789413","https://openalex.org/W2523246573","https://openalex.org/W2594183968","https://openalex.org/W2610148085","https://openalex.org/W2746340587","https://openalex.org/W2765224015","https://openalex.org/W2773987374","https://openalex.org/W2790759781","https://openalex.org/W2790808809","https://openalex.org/W2883583109","https://openalex.org/W2887113605","https://openalex.org/W2900090807","https://openalex.org/W2906506692","https://openalex.org/W2947161483","https://openalex.org/W2949986955","https://openalex.org/W2962398326","https://openalex.org/W2962764565","https://openalex.org/W2969849947","https://openalex.org/W2978927798","https://openalex.org/W3015514050","https://openalex.org/W3083024963","https://openalex.org/W3088615466","https://openalex.org/W3100366369","https://openalex.org/W3100751385","https://openalex.org/W3104956673","https://openalex.org/W3123212791","https://openalex.org/W4214717370","https://openalex.org/W4252520800","https://openalex.org/W4292542951","https://openalex.org/W6742579382"],"related_works":["https://openalex.org/W2181465263","https://openalex.org/W3093969907","https://openalex.org/W3202725889","https://openalex.org/W2232750048","https://openalex.org/W2212726445","https://openalex.org/W4244794230","https://openalex.org/W4389712339","https://openalex.org/W2806540758","https://openalex.org/W2494533090","https://openalex.org/W3082526343"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,15,119,191],"process":[2],"of":[3,17,67,79,88,105,117,121,141,158,160,167,199,239],"placing":[4],"new":[5,146,162],"drugs":[6],"into":[7,221],"the":[8,35,61,65,76,92,100,110,115,122,132,138,156,161,165,168,185,205,230,236,240,257],"market":[9],"is":[10,124,187,253],"time-consuming,":[11],"expensive":[12],"and":[13,64,107,179,233],"complex.":[14],"application":[16],"computational":[18],"methods":[19],"for":[20,75,91],"designing":[21],"molecules":[22,143],"with":[23,47,172,176,201],"bespoke":[24],"properties":[25,37,102,157,208],"can":[26,194],"contribute":[27],"to":[28,38,58,83,113,136,144,154,182],"saving":[29],"resources":[30],"throughout":[31],"this":[32,51,213],"process.":[33],"However,":[34],"fundamental":[36,207],"be":[39],"optimized":[40],"are":[41,152,263],"often":[42],"not":[43],"considered":[44],"or":[45],"conflicting":[46],"each":[48],"other.":[49],"In":[50],"work,":[52],"we":[53],"propose":[54],"a":[55,70,85,127,217,222],"novel":[56],"approach":[57,214],"consider":[59],"both":[60],"biological":[62],"property":[63],"bioavailability":[66],"compounds":[68,90,147],"through":[69],"deep":[71],"reinforcement":[72,173],"learning":[73],"framework":[74,123],"targeted":[77],"generation":[78],"compounds.":[80],"We":[81],"aim":[82],"obtain":[84],"promising":[86],"set":[87,198],"selective":[89],"adenosine":[93],"A2A":[94],"receptor":[95],"and,":[96],"simultaneously,":[97],"that":[98,184],"have":[99],"necessary":[101],"in":[103,245,256],"terms":[104],"solubility":[106],"permeability":[108],"across":[109],"blood-brain":[111],"barrier":[112],"reach":[114],"site":[116],"action.":[118],"cornerstone":[120],"based":[125],"on":[126,225],"recurrent":[128],"neural":[129],"network":[130],"architecture,":[131],"Generator.":[133],"It":[134],"seeks":[135],"learn":[137],"building":[139],"rules":[140],"valid":[142],"sample":[145],"further.":[148],"Also,":[149],"two":[150,206],"Predictors":[151],"trained":[153],"estimate":[155],"interest":[159],"molecules.":[163],"Finally,":[164],"fine-tuning":[166],"Generator":[169,186,193],"was":[170],"performed":[171],"learning,":[174],"integrated":[175],"multi-objective":[177],"optimization":[178],"exploratory":[180],"techniques":[181],"ensure":[183],"adequately":[188],"biased.":[189],"RESULTS:":[190],"biased":[192,209],"generate":[195],"an":[196],"interesting":[197],"molecules,":[200],"approximately":[202],"85%":[203],"having":[204],"as":[210],"desired.":[211],"Thus,":[212],"has":[215],"transformed":[216],"general":[218],"molecule":[219],"generator":[220],"model":[223],"focused":[224],"optimizing":[226],"specific":[227],"objectives.":[228],"Furthermore,":[229],"molecules'":[231],"synthesizability":[232],"drug-likeness":[234],"demonstrate":[235],"potential":[237],"applicability":[238],"de":[241],"novo":[242],"drug":[243],"design":[244],"medicinal":[246],"chemistry.":[247],"AVAILABILITY":[248],"AND":[249],"IMPLEMENTATION:":[250],"All":[251],"code":[252],"publicly":[254],"available":[255,264],"https://github.com/larngroup/De-Novo-Drug-Design.":[258],"SUPPLEMENTARY":[259],"INFORMATION:":[260],"Supplementary":[261],"data":[262],"at":[265],"Bioinformatics":[266],"online.":[267]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":6}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2021-07-19T00:00:00"}
