{"id":"https://openalex.org/W3215957353","doi":"https://doi.org/10.1186/s13321-021-00572-6","title":"MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning","display_name":"MERMAID: an open source automated hit-to-lead method based on deep reinforcement learning","publication_year":2021,"publication_date":"2021-11-27","ids":{"openalex":"https://openalex.org/W3215957353","doi":"https://doi.org/10.1186/s13321-021-00572-6","mag":"3215957353","pmid":"https://pubmed.ncbi.nlm.nih.gov/34838134"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-021-00572-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-021-00572-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-021-00572-6","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/s13321-021-00572-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082435783","display_name":"Daiki Erikawa","orcid":null},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Daiki Erikawa","raw_affiliation_strings":["Department of Computer Science, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, Japan","Department of Computer Science, Tokyo Institute of Technology, 4259\u2013J3\u201323, Nagatsuta-cho, Midori-ku, Yokohama, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, Japan","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Department of Computer Science, Tokyo Institute of Technology, 4259\u2013J3\u201323, Nagatsuta-cho, Midori-ku, Yokohama, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007541895","display_name":"Nobuaki Yasuo","orcid":"https://orcid.org/0000-0002-3114-7895"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Nobuaki Yasuo","raw_affiliation_strings":["Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6-23, 2-12-1, Ookayama, Meguro-ku, Tokyo, Japan","Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6\u201323, 2\u201312\u20131, Ookayama, Meguro-ku, Tokyo, Japan"],"raw_orcid":"https://orcid.org/0000-0002-3114-7895","affiliations":[{"raw_affiliation_string":"Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6-23, 2-12-1, Ookayama, Meguro-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6\u201323, 2\u201312\u20131, Ookayama, Meguro-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I114531698"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015321582","display_name":"Masakazu Sekijima","orcid":"https://orcid.org/0000-0002-3806-9535"},"institutions":[{"id":"https://openalex.org/I114531698","display_name":"Tokyo Institute of Technology","ror":"https://ror.org/0112mx960","country_code":"JP","type":"education","lineage":["https://openalex.org/I114531698"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masakazu Sekijima","raw_affiliation_strings":["Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6-23, 2-12-1, Ookayama, Meguro-ku, Tokyo, Japan. sekijima@c.titech.ac.jp","Department of Computer Science, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, Japan. sekijima@c.titech.ac.jp","Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6\u201323, 2\u201312\u20131, Ookayama, Meguro-ku, Tokyo, Japan"],"raw_orcid":"https://orcid.org/0000-0002-3806-9535","affiliations":[{"raw_affiliation_string":"Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6-23, 2-12-1, Ookayama, Meguro-ku, Tokyo, Japan. sekijima@c.titech.ac.jp","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Department of Computer Science, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, Japan. sekijima@c.titech.ac.jp","institution_ids":["https://openalex.org/I114531698"]},{"raw_affiliation_string":"Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6\u201323, 2\u201312\u20131, Ookayama, Meguro-ku, Tokyo, Japan","institution_ids":["https://openalex.org/I114531698"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5082435783"],"corresponding_institution_ids":["https://openalex.org/I114531698"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":3.0282,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.92418019,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"13","issue":"1","first_page":"94","last_page":"94"},"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":0.9970999956130981,"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9843999743461609,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7842070460319519},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.522876501083374},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5222290754318237},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.4578996002674103},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.44478896260261536},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38991355895996094},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.32055455446243286},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11286613345146179},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10463371872901917}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7842070460319519},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.522876501083374},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5222290754318237},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.4578996002674103},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.44478896260261536},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38991355895996094},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.32055455446243286},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11286613345146179},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10463371872901917},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-021-00572-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-021-00572-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-021-00572-6","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:34838134","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34838134","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:25b685331a2b4355b8bd8e12c68c8c7d","is_oa":true,"landing_page_url":"https://doaj.org/article/25b685331a2b4355b8bd8e12c68c8c7d","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 13, Iss 1, Pp 1-10 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8626955","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8626955","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 Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-021-00572-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-021-00572-6","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-021-00572-6","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":[],"awards":[{"id":"https://openalex.org/G1562415319","display_name":null,"funder_award_id":"JP20am0101112","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G8810219073","display_name":null,"funder_award_id":"20H00620","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3215957353.pdf","grobid_xml":"https://content.openalex.org/works/W3215957353.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1521626043","https://openalex.org/W1528174880","https://openalex.org/W1625390266","https://openalex.org/W1714211023","https://openalex.org/W1998848097","https://openalex.org/W2022998385","https://openalex.org/W2034549041","https://openalex.org/W2064675550","https://openalex.org/W2099471712","https://openalex.org/W2100528947","https://openalex.org/W2110872379","https://openalex.org/W2126316555","https://openalex.org/W2178762325","https://openalex.org/W2529996553","https://openalex.org/W2578240541","https://openalex.org/W2583907533","https://openalex.org/W2755830913","https://openalex.org/W2763220183","https://openalex.org/W2786722833","https://openalex.org/W2805177834","https://openalex.org/W2806351858","https://openalex.org/W2883583109","https://openalex.org/W2911495555","https://openalex.org/W2913087274","https://openalex.org/W2913351693","https://openalex.org/W2914335761","https://openalex.org/W2916487223","https://openalex.org/W2945551948","https://openalex.org/W2956961449","https://openalex.org/W2962764565","https://openalex.org/W2972741532","https://openalex.org/W2996312555","https://openalex.org/W3001935646","https://openalex.org/W3035314354","https://openalex.org/W3043969542","https://openalex.org/W3098269892","https://openalex.org/W3104705366","https://openalex.org/W3104956673","https://openalex.org/W4289436753"],"related_works":["https://openalex.org/W4365211920","https://openalex.org/W3014948380","https://openalex.org/W4380551139","https://openalex.org/W2280377497","https://openalex.org/W3174044702","https://openalex.org/W4238433571","https://openalex.org/W2967848559","https://openalex.org/W4283803360","https://openalex.org/W4317695495","https://openalex.org/W4387506531"],"abstract_inverted_index":{"The":[0,38,203],"hit-to-lead":[1,36,121],"process":[2,89],"makes":[3],"the":[4,8,13,20,35,54,63,88,120,151,174,187,190],"physicochemical":[5],"properties":[6],"of":[7,16,50,57,62,68,90,189,193],"hit":[9],"molecules":[10,106,180],"that":[11,133,181],"show":[12],"desired":[14],"type":[15],"activity":[17],"obtained":[18,172],"in":[19,82],"screening":[21],"assay":[22],"more":[23],"drug-like.":[24],"Deep":[25],"learning-based":[26],"molecular":[27,40,71,85],"generative":[28,72,131],"models":[29,73],"are":[30,93],"expected":[31],"to":[32,34,84,104,116,119],"contribute":[33],"process.":[37,122],"simplified":[39],"input":[41],"line":[42],"entry":[43],"system":[44],"(SMILES),":[45],"which":[46],"is":[47,60,101,206],"a":[48,58,109,129,139,160,169],"string":[49],"alphanumeric":[51],"characters":[52],"representing":[53],"chemical":[55],"structure":[56],"molecule,":[59,111],"one":[61],"most":[64],"commonly":[65],"used":[66],"representations":[67],"molecules,":[69],"and":[70,147,159,177,196],"based":[74],"on":[75],"SMILES":[76,92,118,146,153],"have":[77,127],"achieved":[78],"significant":[79],"success.":[80],"However,":[81],"contrast":[83],"graphs,":[86],"during":[87],"generation,":[91],"not":[94],"considered":[95],"as":[96],"valid":[97],"SMILES.":[98],"Further,":[99],"it":[100,114,149],"quite":[102],"difficult":[103,115],"generate":[105],"starting":[107,137],"from":[108,138,173],"certain":[110,140],"thus":[112],"making":[113],"apply":[117],"In":[123],"this":[124],"study,":[125],"we":[126],"developed":[128],"SMILES-based":[130],"model":[132],"can":[134],"be":[135],"generated":[136,179],"molecule.":[141],"This":[142],"method":[143,167],"generates":[144],"partial":[145],"inserts":[148],"into":[150],"original":[152],"using":[154,168],"Monte":[155],"Carlo":[156],"Tree":[157],"Search":[158],"Recurrent":[161],"Neural":[162],"Network.":[163],"We":[164],"validated":[165],"our":[166],"molecule":[170],"dataset":[171],"ZINC":[175],"database":[176],"successfully":[178],"were":[182],"both":[183],"well":[184],"optimized":[185],"for":[186],"objectives":[188],"quantitative":[191],"estimate":[192],"drug-likeness":[194],"(QED)":[195],"penalized":[197],"octanol-water":[198],"partition":[199],"coefficient":[200],"(PLogP)":[201],"optimization.":[202],"source":[204],"code":[205],"available":[207],"at":[208],"https://github.com/sekijima-lab/mermaid":[209],".":[210]},"counts_by_year":[{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
