{"id":"https://openalex.org/W4313236609","doi":"https://doi.org/10.1093/bioinformatics/btac814","title":"Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer","display_name":"Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer","publication_year":2022,"publication_date":"2022-12-28","ids":{"openalex":"https://openalex.org/W4313236609","doi":"https://doi.org/10.1093/bioinformatics/btac814","pmid":"https://pubmed.ncbi.nlm.nih.gov/36576008"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac814","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac814","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac814/48646689/btac814.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/39/1/btac814/48646689/btac814.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109259917","display_name":"Zhirui Liao","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhirui Liao","raw_affiliation_strings":["School of Computer Science, Fudan University , Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066245750","display_name":"Lei Xie","orcid":"https://orcid.org/0000-0001-9051-2111"},"institutions":[{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lei Xie","raw_affiliation_strings":["Department of Computer Science, Hunter College, The City University of New York , New York, NY 10065, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, The City University of New York , New York, NY 10065, USA","institution_ids":["https://openalex.org/I39694355","https://openalex.org/I174216632"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059001924","display_name":"Hiroshi Mamitsuka","orcid":"https://orcid.org/0000-0002-6607-5617"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"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/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","JP"],"is_corresponding":false,"raw_author_name":"Hiroshi Mamitsuka","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto Prefecture 611-0011, Japan","Department of Computer Science, Aalto University , Espoo 00076, Finland"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University , Uji, Kyoto Prefecture 611-0011, Japan","institution_ids":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"raw_affiliation_string":"Department of Computer Science, Aalto University , Espoo 00076, Finland","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045866167","display_name":"Shanfeng Zhu","orcid":"https://orcid.org/0000-0002-6067-5312"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I2802974365","display_name":"Shanghai Innovative Research Center of Traditional Chinese Medicine","ror":"https://ror.org/01gnagj68","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802974365"]},{"id":"https://openalex.org/I4210085920","display_name":"Shanghai Institute for Science of Science","ror":"https://ror.org/004srxn73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210085920"]},{"id":"https://openalex.org/I4210122302","display_name":"ShangHai JiAi Genetics & IVF Institute","ror":"https://ror.org/02rgbry52","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210122302"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shanfeng Zhu","raw_affiliation_strings":["Institute of Artificial Intelligence Biomedicine, Nanjing University , Nanjing, Jiangsu 210031, China","Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University , Shanghai 200433, China","Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education , Shanghai 200433, China","Shanghai Key Lab of Intelligent Information Processing and Shanghai Institute of Artificial Intelligence Algorithm, Fudan University , Shanghai 200433, China","Shanghai Qi Zhi Institute , Shanghai 200030, China","Zhangjiang Fudan International Innovation Center , Shanghai 200433, China"],"affiliations":[{"raw_affiliation_string":"Institute of Artificial Intelligence Biomedicine, Nanjing University , Nanjing, Jiangsu 210031, China","institution_ids":["https://openalex.org/I881766915"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I4210085920","https://openalex.org/I24943067"]},{"raw_affiliation_string":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Key Lab of Intelligent Information Processing and Shanghai Institute of Artificial Intelligence Algorithm, Fudan University , Shanghai 200433, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Qi Zhi Institute , Shanghai 200030, China","institution_ids":["https://openalex.org/I4210122302"]},{"raw_affiliation_string":"Zhangjiang Fudan International Innovation Center , Shanghai 200433, China","institution_ids":["https://openalex.org/I2802974365"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5045866167"],"corresponding_institution_ids":["https://openalex.org/I24943067","https://openalex.org/I2802974365","https://openalex.org/I4210085920","https://openalex.org/I4210122302","https://openalex.org/I4210164150","https://openalex.org/I881766915"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.1682,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.9292103,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"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":0.996399998664856,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9958000183105469,"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/autoencoder","display_name":"Autoencoder","score":0.7828264236450195},{"id":"https://openalex.org/keywords/scaffold","display_name":"Scaffold","score":0.7562874555587769},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7349916100502014},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.6520581245422363},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5894186496734619},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.5428755879402161},{"id":"https://openalex.org/keywords/generator","display_name":"Generator (circuit theory)","score":0.5139145851135254},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38414478302001953},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34663310647010803},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1549837589263916},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.1275371015071869},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09731143712997437}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.7828264236450195},{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.7562874555587769},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7349916100502014},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.6520581245422363},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5894186496734619},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.5428755879402161},{"id":"https://openalex.org/C2780992000","wikidata":"https://www.wikidata.org/wiki/Q17016113","display_name":"Generator (circuit theory)","level":3,"score":0.5139145851135254},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38414478302001953},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34663310647010803},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1549837589263916},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.1275371015071869},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09731143712997437},{"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/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"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/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","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}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btac814","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac814","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac814/48646689/btac814.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:36576008","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36576008","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:irdb.nii.ac.jp:01221:0006911914","is_oa":true,"landing_page_url":"http://hdl.handle.net/2433/296069","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"host_organization_lineage_names":[],"type":"repository"},"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":"pmh:oai:aaltodoc.aalto.fi:123456789/119774","is_oa":true,"landing_page_url":"https://research.aalto.fi/en/publications/7505bb4c-0135-42a5-b0f3-f35642920891","pdf_url":null,"source":{"id":"https://openalex.org/S4306401663","display_name":"Aaltodoc (Aalto University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9927081","host_organization_name":"Aalto University","host_organization_lineage":["https://openalex.org/I9927081"],"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":null,"raw_type":"publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:9835482","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9835482","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/btac814","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac814","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac814/48646689/btac814.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":[{"id":"https://openalex.org/G7370466132","display_name":null,"funder_award_id":"62272105","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4313236609.pdf","grobid_xml":"https://content.openalex.org/works/W4313236609.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W24659751","https://openalex.org/W1757990252","https://openalex.org/W1924770834","https://openalex.org/W1975147762","https://openalex.org/W1988037271","https://openalex.org/W2016589492","https://openalex.org/W2023818227","https://openalex.org/W2034549041","https://openalex.org/W2043509228","https://openalex.org/W2066273100","https://openalex.org/W2095705004","https://openalex.org/W2155165383","https://openalex.org/W2529996553","https://openalex.org/W2587696209","https://openalex.org/W2612690371","https://openalex.org/W2617635800","https://openalex.org/W2796419445","https://openalex.org/W2809247499","https://openalex.org/W2947950688","https://openalex.org/W2992072991","https://openalex.org/W2992613109","https://openalex.org/W3030948478","https://openalex.org/W3044640842","https://openalex.org/W3087716567","https://openalex.org/W3094553402","https://openalex.org/W3094686696","https://openalex.org/W3098269892","https://openalex.org/W3112113844","https://openalex.org/W3116865743","https://openalex.org/W4252916154","https://openalex.org/W6674330103"],"related_works":["https://openalex.org/W4365211920","https://openalex.org/W3014948380","https://openalex.org/W2470043383","https://openalex.org/W4380551139","https://openalex.org/W2953501176","https://openalex.org/W2965095304","https://openalex.org/W2280377497","https://openalex.org/W3034474024","https://openalex.org/W3174044702","https://openalex.org/W4238433571"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
