{"id":"https://openalex.org/W4379769091","doi":"https://doi.org/10.1186/s13321-023-00726-8","title":"Tora3D: an autoregressive torsion angle prediction model for molecular 3D conformation generation","display_name":"Tora3D: an autoregressive torsion angle prediction model for molecular 3D conformation generation","publication_year":2023,"publication_date":"2023-06-07","ids":{"openalex":"https://openalex.org/W4379769091","doi":"https://doi.org/10.1186/s13321-023-00726-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/37287071"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-023-00726-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00726-8","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00726-8","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/s13321-023-00726-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104265007","display_name":"Zimei Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zimei Zhang","raw_affiliation_strings":["Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230026, Anhui, China","Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230026, Anhui, China","institution_ids":["https://openalex.org/I126520041"]},{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100367305","display_name":"Gang Wang","orcid":"https://orcid.org/0000-0001-6500-5863"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gang Wang","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100448309","display_name":"Rui Li","orcid":"https://orcid.org/0000-0001-5332-2167"},"institutions":[{"id":"https://openalex.org/I161716053","display_name":"China Pharmaceutical University","ror":"https://ror.org/01sfm2718","country_code":"CN","type":"education","lineage":["https://openalex.org/I161716053"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Li","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","School of Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"raw_affiliation_string":"School of Pharmacy, China Pharmaceutical University, 639 Longmian Road, Nanjing, 211198, China","institution_ids":["https://openalex.org/I161716053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108096718","display_name":"Lin Ni","orcid":null},"institutions":[{"id":"https://openalex.org/I131434179","display_name":"Nanjing University of Chinese Medicine","ror":"https://ror.org/04523zj19","country_code":"CN","type":"education","lineage":["https://openalex.org/I131434179"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Ni","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"raw_affiliation_string":"Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China","institution_ids":["https://openalex.org/I131434179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110987617","display_name":"RunZe Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"RunZe Zhang","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082176493","display_name":"Kaiyang Cheng","orcid":"https://orcid.org/0000-0003-1652-4338"},"institutions":[{"id":"https://openalex.org/I131434179","display_name":"Nanjing University of Chinese Medicine","ror":"https://ror.org/04523zj19","country_code":"CN","type":"education","lineage":["https://openalex.org/I131434179"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kaiyang Cheng","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"raw_affiliation_string":"Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China","institution_ids":["https://openalex.org/I131434179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016162911","display_name":"Qun Ren","orcid":"https://orcid.org/0000-0003-0627-761X"},"institutions":[{"id":"https://openalex.org/I131434179","display_name":"Nanjing University of Chinese Medicine","ror":"https://ror.org/04523zj19","country_code":"CN","type":"education","lineage":["https://openalex.org/I131434179"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qun Ren","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"raw_affiliation_string":"Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China","institution_ids":["https://openalex.org/I131434179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026479709","display_name":"Xiangtai Kong","orcid":"https://orcid.org/0000-0002-6257-2560"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangtai Kong","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101323637","display_name":"Shengkun Ni","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shengkun Ni","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040634168","display_name":"Xiaochu Tong","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaochu Tong","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100693619","display_name":"Li Luo","orcid":"https://orcid.org/0000-0003-2667-5615"},"institutions":[{"id":"https://openalex.org/I9916479","display_name":"Air Force Medical University","ror":"https://ror.org/00ms48f15","country_code":"CN","type":"education","lineage":["https://openalex.org/I9916479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Luo","raw_affiliation_strings":["Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710038, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710038, China","institution_ids":["https://openalex.org/I9916479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026206371","display_name":"Dingyan Wang","orcid":"https://orcid.org/0000-0003-2964-7425"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dingyan Wang","raw_affiliation_strings":["Lingang Laboratory, Shanghai, 200031, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lingang Laboratory, Shanghai, 200031, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101484365","display_name":"Xiaojie Lu","orcid":"https://orcid.org/0000-0002-1595-6414"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaojie Lu","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075749706","display_name":"Mingyue Zheng","orcid":"https://orcid.org/0000-0002-3323-3092"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]},{"id":"https://openalex.org/I131434179","display_name":"Nanjing University of Chinese Medicine","ror":"https://ror.org/04523zj19","country_code":"CN","type":"education","lineage":["https://openalex.org/I131434179"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Mingyue Zheng","raw_affiliation_strings":["Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230026, Anhui, China. myzheng@simm.ac.cn","Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China. myzheng@simm.ac.cn","Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China. myzheng@simm.ac.cn","University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China. myzheng@simm.ac.cn","Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230026, Anhui, China. myzheng@simm.ac.cn","institution_ids":["https://openalex.org/I126520041"]},{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China. myzheng@simm.ac.cn","institution_ids":["https://openalex.org/I4210112820"]},{"raw_affiliation_string":"Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China. myzheng@simm.ac.cn","institution_ids":["https://openalex.org/I131434179"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China. myzheng@simm.ac.cn","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046574920","display_name":"Xutong Li","orcid":"https://orcid.org/0000-0001-9547-0643"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xutong Li","raw_affiliation_strings":["Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China. lixutong@simm.ac.cn","University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China. lixutong@simm.ac.cn","Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China. lixutong@simm.ac.cn","institution_ids":["https://openalex.org/I4210112820"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing, 100049, China. lixutong@simm.ac.cn","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5046574920","https://openalex.org/A5075749706"],"corresponding_institution_ids":["https://openalex.org/I126520041","https://openalex.org/I131434179","https://openalex.org/I19820366","https://openalex.org/I4210112820","https://openalex.org/I4210165038"],"apc_list":{"value":1290,"currency":"GBP","value_usd":2190},"apc_paid":{"value":1290,"currency":"GBP","value_usd":2190},"fwci":1.1514,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.80205362,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"15","issue":"1","first_page":"57","last_page":"57"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9958999752998352,"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/autoregressive-model","display_name":"Autoregressive model","score":0.7587592601776123},{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.6804422736167908},{"id":"https://openalex.org/keywords/dihedral-angle","display_name":"Dihedral angle","score":0.6435625553131104},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6300131678581238},{"id":"https://openalex.org/keywords/molecular-conformation","display_name":"Molecular conformation","score":0.42381662130355835},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3513473868370056},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33124250173568726},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.27227941155433655},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.2397877275943756},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1283351182937622}],"concepts":[{"id":"https://openalex.org/C159877910","wikidata":"https://www.wikidata.org/wiki/Q2202883","display_name":"Autoregressive model","level":2,"score":0.7587592601776123},{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.6804422736167908},{"id":"https://openalex.org/C89025888","wikidata":"https://www.wikidata.org/wiki/Q911907","display_name":"Dihedral angle","level":4,"score":0.6435625553131104},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6300131678581238},{"id":"https://openalex.org/C2989255885","wikidata":"https://www.wikidata.org/wiki/Q500256","display_name":"Molecular conformation","level":3,"score":0.42381662130355835},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3513473868370056},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33124250173568726},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.27227941155433655},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.2397877275943756},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1283351182937622},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.0},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-023-00726-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00726-8","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00726-8","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:37287071","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37287071","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:pubmedcentral.nih.gov:10245430","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10245430","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10245430/pdf/13321_2023_Article_726.pdf","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"},{"id":"pmh:oai:doaj.org/article:7084674fa08a498ca5be300cb2521cbb","is_oa":true,"landing_page_url":"https://doaj.org/article/7084674fa08a498ca5be300cb2521cbb","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"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 15, Iss 1, Pp 1-14 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-023-00726-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00726-8","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00726-8","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/G1101904468","display_name":null,"funder_award_id":"82204278","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1618279006","display_name":null,"funder_award_id":"2022YFC3400504","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G492479846","display_name":null,"funder_award_id":"91953203","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5528081863","display_name":null,"funder_award_id":"82273855","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7992132981","display_name":null,"funder_award_id":"2022M720153","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G8039529882","display_name":null,"funder_award_id":"T2225002","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"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4379769091.pdf"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1659842140","https://openalex.org/W1981737096","https://openalex.org/W2015770960","https://openalex.org/W2030971064","https://openalex.org/W2090431249","https://openalex.org/W2147421370","https://openalex.org/W2244785476","https://openalex.org/W2726184500","https://openalex.org/W2761786744","https://openalex.org/W2806664897","https://openalex.org/W2911847761","https://openalex.org/W2931367569","https://openalex.org/W2968734407","https://openalex.org/W3034806393","https://openalex.org/W3105259638","https://openalex.org/W3119095170","https://openalex.org/W3136399186","https://openalex.org/W4210756221","https://openalex.org/W4220790075","https://openalex.org/W4221149941","https://openalex.org/W4281553035","https://openalex.org/W4300109386"],"related_works":["https://openalex.org/W2148970764","https://openalex.org/W2011402683","https://openalex.org/W2051003498","https://openalex.org/W315880741","https://openalex.org/W2054247990","https://openalex.org/W2061647725","https://openalex.org/W2068727511","https://openalex.org/W1120485117","https://openalex.org/W4379769091","https://openalex.org/W2327429313"],"abstract_inverted_index":{"Three-dimensional":[0],"(3D)":[1],"conformations":[2,57,81,172],"of":[3,14,66,69,92,130,169,182],"a":[4,64,115,179],"small":[5],"molecule":[6],"profoundly":[7],"affect":[8],"its":[9,21],"binding":[10],"to":[11,30,103,106,123,126,138,178],"the":[12,16,33,56,79,101,108,121,124,128,143,166],"target":[13],"interest,":[15],"resulting":[17],"biological":[18],"effects,":[19],"and":[20,77,147,149,154,173],"disposition":[22],"in":[23,58,142,156],"living":[24],"organisms,":[25],"but":[26],"it":[27],"is":[28,100],"challenging":[29],"accurately":[31],"characterize":[32],"conformational":[34,97,151],"ensemble":[35],"experimentally.":[36],"Here,":[37],"we":[38,113],"proposed":[39],"an":[40,59,73,157],"autoregressive":[41,75],"torsion":[42,67],"angle":[43],"prediction":[44],"model":[45],"Tora3D":[46,62,134,161],"for":[47,165],"molecular":[48,171,175],"3D":[49,80],"conformer":[50],"generation.":[51,110],"Rather":[52],"than":[53],"directly":[54],"predicting":[55],"end-to-end":[60],"way,":[61],"predicts":[63],"set":[65],"angles":[68],"rotatable":[70],"bonds":[71],"by":[72],"interpretable":[74,158],"method":[76,94],"reconstructs":[78],"from":[82],"them,":[83],"which":[84],"keeps":[85],"structural":[86],"validity":[87],"during":[88],"reconstruction.":[89],"Another":[90],"advancement":[91],"our":[93],"over":[95],"other":[96],"generation":[98,168],"methods":[99],"ability":[102],"use":[104],"energy":[105],"guide":[107],"conformation":[109],"In":[111],"addition,":[112],"propose":[114],"new":[116],"message-passing":[117],"mechanism":[118],"that":[119],"applies":[120],"Transformer":[122],"graph":[125],"solve":[127],"difficulty":[129],"remote":[131],"message":[132],"passing.":[133],"shows":[135],"superior":[136],"performance":[137],"prior":[139],"computational":[140],"models":[141],"trade-off":[144],"between":[145],"accuracy":[146],"efficiency,":[148],"ensures":[150],"validity,":[152],"accuracy,":[153],"diversity":[155],"way.":[159],"Overall,":[160],"can":[162],"be":[163],"used":[164],"quick":[167],"diverse":[170],"3D-based":[174],"representation,":[176],"contributing":[177],"wide":[180],"range":[181],"downstream":[183],"drug":[184],"design":[185],"tasks.":[186]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}