{"id":"https://openalex.org/W4324129409","doi":"https://doi.org/10.1093/bioinformatics/btad122","title":"Accurate and efficient protein sequence design through learning concise local environment of residues","display_name":"Accurate and efficient protein sequence design through learning concise local environment of residues","publication_year":2023,"publication_date":"2023-03-01","ids":{"openalex":"https://openalex.org/W4324129409","doi":"https://doi.org/10.1093/bioinformatics/btad122","pmid":"https://pubmed.ncbi.nlm.nih.gov/36916746"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad122","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad122","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad122/49572012/btad122.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad122/49572012/btad122.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074965518","display_name":"Bin Huang","orcid":"https://orcid.org/0000-0001-7704-9601"},"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/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"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":"Bin Huang","raw_affiliation_strings":["Key Lab of Intelligent Information Processing, SKLP, Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China","University of Chinese Academy of Sciences , Beijing 100110, China"],"raw_orcid":"https://orcid.org/0000-0001-7704-9601","affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, SKLP, Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , Beijing 100110, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049987263","display_name":"Tingwen Fan","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/I4210134982","display_name":"Institute of Microbiology","ror":"https://ror.org/047yhep71","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210134982"]},{"id":"https://openalex.org/I4391767942","display_name":"State Key Laboratory of Mycology","ror":"https://ror.org/01zfc7m08","country_code":null,"type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210134982","https://openalex.org/I4391767942"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tingwen Fan","raw_affiliation_strings":["Key Lab of Microbial Physiological & Metabolic Engineering, State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Microbial Physiological & Metabolic Engineering, State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China","institution_ids":["https://openalex.org/I4210134982","https://openalex.org/I19820366","https://openalex.org/I4391767942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100688355","display_name":"Kaiyue Wang","orcid":"https://orcid.org/0000-0002-3218-7151"},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]},{"id":"https://openalex.org/I890469752","display_name":"Ministry of Industry and Information Technology","ror":"https://ror.org/0385nmy68","country_code":"CN","type":"government","lineage":["https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kaiyue Wang","raw_affiliation_strings":["Beijing Advanced Innovation Center for Big Data-based Precision Medicine, School of Engineering Medicine, Beihang University , Beijing 100083, China","Key Laboratory of Big Data-based Precision Medicine (Beihang University), Ministry of Industry and Information Technology of the People\u2019s Republic of China , Beijing 100083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Advanced Innovation Center for Big Data-based Precision Medicine, School of Engineering Medicine, Beihang University , Beijing 100083, China","institution_ids":["https://openalex.org/I82880672"]},{"raw_affiliation_string":"Key Laboratory of Big Data-based Precision Medicine (Beihang University), Ministry of Industry and Information Technology of the People\u2019s Republic of China , Beijing 100083, China","institution_ids":["https://openalex.org/I890469752","https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060273621","display_name":"Haicang Zhang","orcid":"https://orcid.org/0000-0001-6268-4258"},"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/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"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":"Haicang Zhang","raw_affiliation_strings":["Key Lab of Intelligent Information Processing, SKLP, Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China","University of Chinese Academy of Sciences , Beijing 100110, China","Zhongke Big Data Academy , Zhengzhou, Henan 450046, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, SKLP, Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , Beijing 100110, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Zhongke Big Data Academy , Zhengzhou, Henan 450046, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083737928","display_name":"Chungong Yu","orcid":"https://orcid.org/0000-0003-3025-3415"},"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/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"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":"Chungong Yu","raw_affiliation_strings":["Key Lab of Intelligent Information Processing, SKLP, Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China","University of Chinese Academy of Sciences , Beijing 100110, China","Zhongke Big Data Academy , Zhengzhou, Henan 450046, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, SKLP, Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , Beijing 100110, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Zhongke Big Data Academy , Zhengzhou, Henan 450046, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013341072","display_name":"Shuyu Nie","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/I4210134982","display_name":"Institute of Microbiology","ror":"https://ror.org/047yhep71","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210134982"]},{"id":"https://openalex.org/I43337087","display_name":"Hebei University","ror":"https://ror.org/01p884a79","country_code":"CN","type":"education","lineage":["https://openalex.org/I43337087"]},{"id":"https://openalex.org/I4391767942","display_name":"State Key Laboratory of Mycology","ror":"https://ror.org/01zfc7m08","country_code":null,"type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210134982","https://openalex.org/I4391767942"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuyu Nie","raw_affiliation_strings":["Key Lab of Microbial Physiological & Metabolic Engineering, State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China","School of Life Sciences, Hebei University , Baoding, Hebei 071002, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Microbial Physiological & Metabolic Engineering, State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China","institution_ids":["https://openalex.org/I4210134982","https://openalex.org/I19820366","https://openalex.org/I4391767942"]},{"raw_affiliation_string":"School of Life Sciences, Hebei University , Baoding, Hebei 071002, China","institution_ids":["https://openalex.org/I43337087"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023973881","display_name":"Yangshuo Qi","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/I4210134982","display_name":"Institute of Microbiology","ror":"https://ror.org/047yhep71","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210134982"]},{"id":"https://openalex.org/I43337087","display_name":"Hebei University","ror":"https://ror.org/01p884a79","country_code":"CN","type":"education","lineage":["https://openalex.org/I43337087"]},{"id":"https://openalex.org/I4391767942","display_name":"State Key Laboratory of Mycology","ror":"https://ror.org/01zfc7m08","country_code":null,"type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210134982","https://openalex.org/I4391767942"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yangshuo Qi","raw_affiliation_strings":["Key Lab of Microbial Physiological & Metabolic Engineering, State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China","School of Life Sciences, Hebei University , Baoding, Hebei 071002, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Microbial Physiological & Metabolic Engineering, State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China","institution_ids":["https://openalex.org/I4210134982","https://openalex.org/I19820366","https://openalex.org/I4391767942"]},{"raw_affiliation_string":"School of Life Sciences, Hebei University , Baoding, Hebei 071002, China","institution_ids":["https://openalex.org/I43337087"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021041719","display_name":"Wei\u2010Mou Zheng","orcid":"https://orcid.org/0000-0001-6546-2917"},"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/I4210125404","display_name":"Institute of Theoretical Physics","ror":"https://ror.org/02xtbq882","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210125404"]},{"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":"Wei-Mou Zheng","raw_affiliation_strings":["Institute of Theoretical Physics, Chinese Academy of Sciences , Beijing 100190, China","University of Chinese Academy of Sciences , Beijing 100110, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Theoretical Physics, Chinese Academy of Sciences , Beijing 100190, China","institution_ids":["https://openalex.org/I4210125404","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , Beijing 100110, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049458722","display_name":"Jian Han","orcid":"https://orcid.org/0000-0003-3930-0003"},"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/I4210134982","display_name":"Institute of Microbiology","ror":"https://ror.org/047yhep71","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210134982"]},{"id":"https://openalex.org/I4391767942","display_name":"State Key Laboratory of Mycology","ror":"https://ror.org/01zfc7m08","country_code":null,"type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210134982","https://openalex.org/I4391767942"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Han","raw_affiliation_strings":["Key Lab of Microbial Physiological & Metabolic Engineering, State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Microbial Physiological & Metabolic Engineering, State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China","institution_ids":["https://openalex.org/I4210134982","https://openalex.org/I19820366","https://openalex.org/I4391767942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009343088","display_name":"Zheng Fan","orcid":"https://orcid.org/0000-0002-7542-3134"},"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/I4210134982","display_name":"Institute of Microbiology","ror":"https://ror.org/047yhep71","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210134982"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zheng Fan","raw_affiliation_strings":["Institutional Center for Shared Technologies and Facilities, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China"],"raw_orcid":"https://orcid.org/0000-0002-7542-3134","affiliations":[{"raw_affiliation_string":"Institutional Center for Shared Technologies and Facilities, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210134982"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108903761","display_name":"Shiwei Sun","orcid":"https://orcid.org/0000-0002-0351-3720"},"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/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"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":"Shiwei Sun","raw_affiliation_strings":["Key Lab of Intelligent Information Processing, SKLP, Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China","University of Chinese Academy of Sciences , Beijing 100110, China","Zhongke Big Data Academy , Zhengzhou, Henan 450046, China"],"raw_orcid":"https://orcid.org/0000-0002-0351-3720","affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, SKLP, Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , Beijing 100110, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Zhongke Big Data Academy , Zhengzhou, Henan 450046, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100698459","display_name":"Sheng Ye","orcid":"https://orcid.org/0000-0003-2314-2856"},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]},{"id":"https://openalex.org/I890469752","display_name":"Ministry of Industry and Information Technology","ror":"https://ror.org/0385nmy68","country_code":"CN","type":"government","lineage":["https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Sheng Ye","raw_affiliation_strings":["Beijing Advanced Innovation Center for Big Data-based Precision Medicine, School of Engineering Medicine, Beihang University , Beijing 100083, China","Key Laboratory of Big Data-based Precision Medicine (Beihang University), Ministry of Industry and Information Technology of the People\u2019s Republic of China , Beijing 100083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Advanced Innovation Center for Big Data-based Precision Medicine, School of Engineering Medicine, Beihang University , Beijing 100083, China","institution_ids":["https://openalex.org/I82880672"]},{"raw_affiliation_string":"Key Laboratory of Big Data-based Precision Medicine (Beihang University), Ministry of Industry and Information Technology of the People\u2019s Republic of China , Beijing 100083, China","institution_ids":["https://openalex.org/I890469752","https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101104010","display_name":"Huaiyi Yang","orcid":"https://orcid.org/0000-0003-2196-7811"},"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/I4210134982","display_name":"Institute of Microbiology","ror":"https://ror.org/047yhep71","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210134982"]},{"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"]},{"id":"https://openalex.org/I4391767942","display_name":"State Key Laboratory of Mycology","ror":"https://ror.org/01zfc7m08","country_code":null,"type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210134982","https://openalex.org/I4391767942"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Huaiyi Yang","raw_affiliation_strings":["Key Lab of Microbial Physiological & Metabolic Engineering, State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China","University of Chinese Academy of Sciences , Beijing 100110, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Microbial Physiological & Metabolic Engineering, State Key Lab of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China","institution_ids":["https://openalex.org/I4210134982","https://openalex.org/I19820366","https://openalex.org/I4391767942"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , Beijing 100110, China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076729236","display_name":"Dongbo Bu","orcid":"https://orcid.org/0000-0003-4119-4238"},"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/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]},{"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":"Dongbo Bu","raw_affiliation_strings":["Key Lab of Intelligent Information Processing, SKLP, Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China","University of Chinese Academy of Sciences , Beijing 100110, China","Zhongke Big Data Academy , Zhengzhou, Henan 450046, China"],"raw_orcid":"https://orcid.org/0000-0003-4119-4238","affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, SKLP, Institute of Computing Technology, Chinese Academy of Sciences , Beijing 100190, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences , Beijing 100110, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Zhongke Big Data Academy , Zhengzhou, Henan 450046, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5076729236","https://openalex.org/A5100698459","https://openalex.org/A5101104010"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210090176","https://openalex.org/I4210134982","https://openalex.org/I4210165038","https://openalex.org/I4391767942","https://openalex.org/I82880672","https://openalex.org/I890469752"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.7091,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.95467069,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"39","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7892000079154968,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7892000079154968,"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/T11162","display_name":"Enzyme Structure and Function","score":0.07429999858140945,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.032499998807907104,"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/sequence","display_name":"Sequence (biology)","score":0.6642491817474365},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6169565320014954},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.5247683525085449},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3238946795463562},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2679385542869568},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20189911127090454},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15399929881095886}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6642491817474365},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6169565320014954},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.5247683525085449},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3238946795463562},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2679385542869568},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20189911127090454},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15399929881095886}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad122","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad122","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad122/49572012/btad122.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:36916746","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36916746","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:10027430","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10027430","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10027430/pdf/btad122.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad122","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad122","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad122/49572012/btad122.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G1887041509","display_name":null,"funder_award_id":"32271297","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4314963621","display_name":null,"funder_award_id":"62072435","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7924934264","display_name":null,"funder_award_id":"82130055","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8671994309","display_name":null,"funder_award_id":"YJKYYQ20210032","funder_id":"https://openalex.org/F4320321133","funder_display_name":"Chinese Academy of Sciences"},{"id":"https://openalex.org/G975092767","display_name":null,"funder_award_id":"2020YFA0907000","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program 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/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"},{"id":"https://openalex.org/F4320322847","display_name":"Youth Innovation Promotion Association of the Chinese Academy of Sciences","ror":"https://ror.org/031141b54"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335892","display_name":"Youth Innovation Promotion Association","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W95014119","https://openalex.org/W1724277458","https://openalex.org/W1969644422","https://openalex.org/W1995808589","https://openalex.org/W2040299410","https://openalex.org/W2052277371","https://openalex.org/W2059681116","https://openalex.org/W2066381187","https://openalex.org/W2098084671","https://openalex.org/W2123850444","https://openalex.org/W2162061338","https://openalex.org/W2606439133","https://openalex.org/W2790952361","https://openalex.org/W2802215780","https://openalex.org/W2899573458","https://openalex.org/W2908391177","https://openalex.org/W2954253694","https://openalex.org/W2991877021","https://openalex.org/W2995514860","https://openalex.org/W2996986155","https://openalex.org/W2997234557","https://openalex.org/W3010339412","https://openalex.org/W3023242404","https://openalex.org/W3088578860","https://openalex.org/W3146944767","https://openalex.org/W3156850097","https://openalex.org/W3157271872","https://openalex.org/W3170217324","https://openalex.org/W3177828909","https://openalex.org/W3216341763","https://openalex.org/W4210861939","https://openalex.org/W4283390570","https://openalex.org/W4286491305","https://openalex.org/W4320015740"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"MOTIVATION:":[0],"Computational":[1],"protein":[2,11,34,125],"sequence":[3,35,97],"design":[4,16,111],"has":[5],"been":[6],"widely":[7],"applied":[8,108],"in":[9,170],"rational":[10],"engineering":[12],"and":[13,18,30,49,62,117,165,180],"increasing":[14],"the":[15,45,55,74,137,168,191],"accuracy":[17],"efficiency":[19],"is":[20,204],"highly":[21],"desired.":[22],"RESULTS:":[23],"Here,":[24],"we":[25],"present":[26],"ProDESIGN-LE,":[27],"an":[28,78,157],"accurate":[29],"efficient":[31],"approach":[32],"to":[33,53,76,110],"design.":[36],"ProDESIGN-LE":[37,72,109,151,203],"adopts":[38],"a":[39,51,68,95,141],"concise":[40],"but":[41],"informative":[42],"representation":[43],"of":[44,60,202],"residue's":[46],"local":[47,58,88,105],"environment":[48,59,89],"trains":[50],"transformer":[52,75],"learn":[54],"correlation":[56],"between":[57],"residues":[61,100],"their":[63,104,132],"amino":[64],"acid":[65],"types.":[66],"For":[67],"target":[69,138],"backbone":[70],"structure,":[71,92],"uses":[73],"assign":[77],"appropriate":[79],"residue":[80],"type":[81,161],"for":[82,113,156],"each":[83],"position":[84],"based":[85],"on":[86,126],"its":[87],"within":[90,121],"this":[91],"eventually":[93],"acquiring":[94],"designed":[96,129],"with":[98,103,140,185,190],"all":[99],"fitting":[101],"well":[102],"environments.":[106],"We":[107,147],"sequences":[112,155],"68":[114],"naturally":[115],"occurring":[116],"129":[118],"hallucinated":[119],"proteins":[120,130,169],"20":[122],"s":[123],"per":[124],"average.":[127],"The":[128,199],"have":[131],"predicted":[133],"structures":[134,139],"perfectly":[135],"resembling":[136],"state-of-the-art":[142],"average":[143],"TM-score":[144],"exceeding":[145],"0.80.":[146],"further":[148],"experimentally":[149],"validated":[150],"by":[152],"designing":[153],"five":[154],"enzyme,":[158],"chloramphenicol":[159],"O-acetyltransferase":[160],"III":[162,194],"(CAT":[163],"III),":[164],"recombinantly":[166],"expressing":[167],"Escherichia":[171],"coli.":[172],"Of":[173],"these":[174],"proteins,":[175],"three":[176],"exhibited":[177],"excellent":[178],"solubility,":[179],"one":[181],"yielded":[182],"monomeric":[183],"species":[184],"circular":[186],"dichroism":[187],"spectra":[188],"consistent":[189],"natural":[192],"CAT":[193],"protein.":[195],"AVAILABILITY":[196],"AND":[197],"IMPLEMENTATION:":[198],"source":[200],"code":[201],"available":[205],"at":[206],"https://github.com/bigict/ProDESIGN-LE.":[207]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
