{"id":"https://openalex.org/W4408102402","doi":"https://doi.org/10.1021/acs.jctc.4c01246","title":"Computation-Enabled Structure-Based Discovery of Potent Binders for Small-Molecule Aptamers","display_name":"Computation-Enabled Structure-Based Discovery of Potent Binders for Small-Molecule Aptamers","publication_year":2025,"publication_date":"2025-03-03","ids":{"openalex":"https://openalex.org/W4408102402","doi":"https://doi.org/10.1021/acs.jctc.4c01246","pmid":"https://pubmed.ncbi.nlm.nih.gov/40029701"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jctc.4c01246","doi":"https://doi.org/10.1021/acs.jctc.4c01246","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jctc.4c01246","pdf_url":null,"source":{"id":"https://openalex.org/S189701308","display_name":"Journal of Chemical Theory and Computation","issn_l":"1549-9618","issn":["1549-9618","1549-9626"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Theory and Computation","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025033449","display_name":"Qingtong Zhou","orcid":"https://orcid.org/0000-0001-8124-3079","observed_orcids":["https://orcid.org/0000-0001-8124-3079"]},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"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/I2801556517","display_name":"Ruijin Hospital","ror":"https://ror.org/01hv94n30","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2801556517"]},{"id":"https://openalex.org/I4392021104","display_name":"State Key Laboratory of Medical Genomics","ror":"https://ror.org/04m0qde81","country_code":"CN","type":"facility","lineage":["https://openalex.org/I183067930","https://openalex.org/I4392021104"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qingtong Zhou","raw_affiliation_strings":["Department of Pharmacology, School of Basic Medical Sciences","Fudan University","Research Center for Deepsea Bioresources","Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital","Shanghai Jiao Tong University School of Medicine","Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China","Research Center for Deepsea Bioresources, Sanya, Hainan 572025, China","Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"],"raw_orcid":"https://orcid.org/0000-0001-8124-3079","affiliations":[{"raw_affiliation_string":"Department of Pharmacology, School of Basic Medical Sciences","institution_ids":[]},{"raw_affiliation_string":"Fudan University","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Research Center for Deepsea Bioresources","institution_ids":[]},{"raw_affiliation_string":"Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital","institution_ids":["https://openalex.org/I2801556517","https://openalex.org/I4392021104"]},{"raw_affiliation_string":"Shanghai Jiao Tong University School of Medicine","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China","institution_ids":["https://openalex.org/I133868755","https://openalex.org/I24943067"]},{"raw_affiliation_string":"Research Center for Deepsea Bioresources, Sanya, Hainan 572025, China","institution_ids":[]},{"raw_affiliation_string":"Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China","institution_ids":["https://openalex.org/I183067930","https://openalex.org/I2801556517","https://openalex.org/I4392021104"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100360367","display_name":"Zheng Zhang","orcid":"https://orcid.org/0000-0002-8438-1829","observed_orcids":["https://orcid.org/0000-0002-8438-1829"]},"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/I4405261136","display_name":"Hangzhou Institute of Medicine, Chinese Academy of Sciences","ror":"https://ror.org/04vs9wp72","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366","https://openalex.org/I4405258660","https://openalex.org/I4405261136"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zheng Zhang","raw_affiliation_strings":["Chinese Academy of Sciences","The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM)","The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences","institution_ids":["https://openalex.org/I19820366"]},{"raw_affiliation_string":"The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM)","institution_ids":["https://openalex.org/I4405261136"]},{"raw_affiliation_string":"The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4405261136"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071169851","display_name":"Ling Gao","orcid":"https://orcid.org/0000-0002-4501-5412","observed_orcids":["https://orcid.org/0000-0002-4501-5412"]},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ling Gao","raw_affiliation_strings":["Jiangnan University","The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology","The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China"],"raw_orcid":"https://orcid.org/0000-0002-4501-5412","affiliations":[{"raw_affiliation_string":"Jiangnan University","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology","institution_ids":[]},{"raw_affiliation_string":"The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075010545","display_name":"Guanyi Li","orcid":"https://orcid.org/0000-0003-2790-9962","observed_orcids":["https://orcid.org/0000-0003-2790-9962"]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guanyi Li","raw_affiliation_strings":["Research Center for Deepsea Bioresources","School of Pharmaceutical Sciences","Shanghai Jiao Tong University","Research Center for Deepsea Bioresources, Sanya, Hainan 572025, China","School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Deepsea Bioresources","institution_ids":[]},{"raw_affiliation_string":"School of Pharmaceutical Sciences","institution_ids":[]},{"raw_affiliation_string":"Shanghai Jiao Tong University","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Research Center for Deepsea Bioresources, Sanya, Hainan 572025, China","institution_ids":[]},{"raw_affiliation_string":"School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100333798","display_name":"Yue Zhang","orcid":"https://orcid.org/0000-0003-3443-7721","observed_orcids":["https://orcid.org/0000-0003-3443-7721"]},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yue Zhang","raw_affiliation_strings":["Jiangnan University","The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology","The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jiangnan University","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology","institution_ids":[]},{"raw_affiliation_string":"The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102865924","display_name":"Weili Yang","orcid":"https://orcid.org/0000-0003-3646-7772","observed_orcids":["https://orcid.org/0000-0003-3646-7772"]},"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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weili Yang","raw_affiliation_strings":["School of Life Science","University of Science and Technology of China","School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Science","institution_ids":[]},{"raw_affiliation_string":"University of Science and Technology of China","institution_ids":["https://openalex.org/I126520041"]},{"raw_affiliation_string":"School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101981233","display_name":"Yaxue Zhao","orcid":"https://orcid.org/0000-0002-5963-9779","observed_orcids":["https://orcid.org/0000-0002-5963-9779"]},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaxue Zhao","raw_affiliation_strings":["School of Pharmaceutical Sciences","Shanghai Jiao Tong University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences","institution_ids":[]},{"raw_affiliation_string":"Shanghai Jiao Tong University","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066262614","display_name":"Dehua Yang","orcid":"https://orcid.org/0000-0003-3028-3243","observed_orcids":["https://orcid.org/0000-0003-3028-3243"]},"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/I4210126186","display_name":"National Center for Drug Screening","ror":"https://ror.org/0384ghs60","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210126186"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dehua Yang","raw_affiliation_strings":["Chinese Academy of Sciences (CAS)","Research Center for Deepsea Bioresources","The National Center for Drug Screening and State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica","Research Center for Deepsea Bioresources, Sanya, Hainan 572025, China","The National Center for Drug Screening and State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China"],"raw_orcid":"https://orcid.org/0000-0003-3028-3243","affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences (CAS)","institution_ids":["https://openalex.org/I19820366"]},{"raw_affiliation_string":"Research Center for Deepsea Bioresources","institution_ids":[]},{"raw_affiliation_string":"The National Center for Drug Screening and State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I4210126186"]},{"raw_affiliation_string":"Research Center for Deepsea Bioresources, Sanya, Hainan 572025, China","institution_ids":[]},{"raw_affiliation_string":"The National Center for Drug Screening and State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210112820","https://openalex.org/I4210126186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100683205","display_name":"Ming\u2010Wei Wang","orcid":"https://orcid.org/0000-0001-6550-9017","observed_orcids":["https://orcid.org/0000-0001-6550-9017","https://orcid.org/0000-0003-3028-3243"]},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"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/I2801556517","display_name":"Ruijin Hospital","ror":"https://ror.org/01hv94n30","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2801556517"]},{"id":"https://openalex.org/I4392021104","display_name":"State Key Laboratory of Medical Genomics","ror":"https://ror.org/04m0qde81","country_code":"CN","type":"facility","lineage":["https://openalex.org/I183067930","https://openalex.org/I4392021104"]},{"id":"https://openalex.org/I79731167","display_name":"Hainan Medical University","ror":"https://ror.org/004eeze55","country_code":"CN","type":"education","lineage":["https://openalex.org/I79731167"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ming-Wei Wang","raw_affiliation_strings":["Department of Pharmacology, School of Basic Medical Sciences","Engineering Research Center of Tropical Medicine Innovation and Transformation of Ministry of Education, School of Pharmacy","Fudan University","Research Center for Deepsea Bioresources","Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital","Shanghai Jiao Tong University School of Medicine","Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China","Engineering Research Center of Tropical Medicine Innovation and Transformation of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou 570228, China","Research Center for Deepsea Bioresources, Sanya, Hainan 572025, China","Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"],"raw_orcid":"https://orcid.org/0000-0001-6550-9017","affiliations":[{"raw_affiliation_string":"Department of Pharmacology, School of Basic Medical Sciences","institution_ids":[]},{"raw_affiliation_string":"Engineering Research Center of Tropical Medicine Innovation and Transformation of Ministry of Education, School of Pharmacy","institution_ids":[]},{"raw_affiliation_string":"Fudan University","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Research Center for Deepsea Bioresources","institution_ids":[]},{"raw_affiliation_string":"Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital","institution_ids":["https://openalex.org/I2801556517","https://openalex.org/I4392021104"]},{"raw_affiliation_string":"Shanghai Jiao Tong University School of Medicine","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China","institution_ids":["https://openalex.org/I133868755","https://openalex.org/I24943067"]},{"raw_affiliation_string":"Engineering Research Center of Tropical Medicine Innovation and Transformation of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou 570228, China","institution_ids":["https://openalex.org/I79731167"]},{"raw_affiliation_string":"Research Center for Deepsea Bioresources, Sanya, Hainan 572025, China","institution_ids":[]},{"raw_affiliation_string":"Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China","institution_ids":["https://openalex.org/I183067930","https://openalex.org/I2801556517","https://openalex.org/I4392021104"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046848255","display_name":"Zhaofeng Luo","orcid":"https://orcid.org/0000-0002-2740-8204","observed_orcids":["https://orcid.org/0000-0002-2740-8204"]},"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/I4405261136","display_name":"Hangzhou Institute of Medicine, Chinese Academy of Sciences","ror":"https://ror.org/04vs9wp72","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366","https://openalex.org/I4405258660","https://openalex.org/I4405261136"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhaofeng Luo","raw_affiliation_strings":["Chinese Academy of Sciences","The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM)","The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China"],"raw_orcid":"https://orcid.org/0000-0002-2740-8204","affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences","institution_ids":["https://openalex.org/I19820366"]},{"raw_affiliation_string":"The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM)","institution_ids":["https://openalex.org/I4405261136"]},{"raw_affiliation_string":"The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Aptamer Selection Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4405261136"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075876792","display_name":"Xiaole Xia","orcid":"https://orcid.org/0000-0002-9063-9507","observed_orcids":["https://orcid.org/0000-0002-9063-9507"]},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]},{"id":"https://openalex.org/I132369690","display_name":"Tianjin University of Science and Technology","ror":"https://ror.org/018rbtf37","country_code":"CN","type":"education","lineage":["https://openalex.org/I132369690"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaole Xia","raw_affiliation_strings":["College of Food Science and Engineering","Jiangnan University","The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology","Tianjin University of Science and Technology","College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China","The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China"],"raw_orcid":"https://orcid.org/0000-0002-9063-9507","affiliations":[{"raw_affiliation_string":"College of Food Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Jiangnan University","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology","institution_ids":[]},{"raw_affiliation_string":"Tianjin University of Science and Technology","institution_ids":["https://openalex.org/I132369690"]},{"raw_affiliation_string":"College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China","institution_ids":["https://openalex.org/I132369690"]},{"raw_affiliation_string":"The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China","institution_ids":["https://openalex.org/I111599522"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5025033449","https://openalex.org/A5046848255","https://openalex.org/A5075876792","https://openalex.org/A5100683205"],"corresponding_institution_ids":["https://openalex.org/I111599522","https://openalex.org/I132369690","https://openalex.org/I133868755","https://openalex.org/I183067930","https://openalex.org/I19820366","https://openalex.org/I24943067","https://openalex.org/I2801556517","https://openalex.org/I4392021104","https://openalex.org/I4405261136","https://openalex.org/I79731167"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":0.8765,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.67042096,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"21","issue":"6","first_page":"3216","last_page":"3230"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9404000043869019,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9404000043869019,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.037300001829862595,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.004600000102072954,"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/aptamer-target-interactions","display_name":"aptamer-target interaction","score":0.6700000166893005},{"id":"https://openalex.org/keywords/aptamer-specificity","display_name":"aptamer specificity","score":0.8190000057220459},{"id":"https://openalex.org/keywords/norfloxacin","display_name":"norfloxacin","score":0.9350000023841858},{"id":"https://openalex.org/keywords/guanethidine","display_name":"guanethidine","score":0.8880000114440918},{"id":"https://openalex.org/keywords/off-target-binding","display_name":"off-target binding","score":0.6610000133514404}],"concepts":[{"id":"https://openalex.org/C128972844","wikidata":"https://www.wikidata.org/wiki/Q418722","display_name":"Aptamer","level":2,"score":0.7236658334732056},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5637790560722351},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5355353951454163},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.4813978672027588},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46202167868614197},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3861011564731598},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.3848132789134979},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3592783212661743},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3316025733947754},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2044316828250885},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.1894717514514923},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.14530879259109497},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07512101531028748},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D052157","descriptor_name":"Aptamers, Nucleotide","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jctc.4c01246","doi":"https://doi.org/10.1021/acs.jctc.4c01246","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jctc.4c01246","pdf_url":null,"source":{"id":"https://openalex.org/S189701308","display_name":"Journal of Chemical Theory and Computation","issn_l":"1549-9618","issn":["1549-9618","1549-9626"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Theory and Computation","raw_type":"journal-article"},{"id":"pmid:40029701","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40029701","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,"listed_in":[],"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 chemical theory and computation","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1313489940","display_name":null,"funder_award_id":"(111-2-06","funder_id":"https://openalex.org/F4320335785","funder_display_name":"Project 211"},{"id":"https://openalex.org/G1898721675","display_name":null,"funder_award_id":"ZDKJ2021028","funder_id":"https://openalex.org/F4320335957","funder_display_name":"Major Science and Technology Project of Hainan Province"},{"id":"https://openalex.org/G5809980136","display_name":null,"funder_award_id":"2023C03043","funder_id":"https://openalex.org/F8142712028","funder_display_name":"Key Research and Development Program of Zhejiang Province"},{"id":"https://openalex.org/G6569680945","display_name":null,"funder_award_id":"2021YFA0910200","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7993491815","display_name":null,"funder_award_id":"21704064","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/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335785","display_name":"Project 211","ror":null},{"id":"https://openalex.org/F4320335957","display_name":"Major Science and Technology Project of Hainan Province","ror":null},{"id":"https://openalex.org/F8142712028","display_name":"Key Research and Development Program of Zhejiang Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":78,"referenced_works":["https://openalex.org/W65628087","https://openalex.org/W1703081596","https://openalex.org/W1965762256","https://openalex.org/W1968984443","https://openalex.org/W1976067984","https://openalex.org/W1976499671","https://openalex.org/W1987864397","https://openalex.org/W1989020100","https://openalex.org/W1990263194","https://openalex.org/W2014326137","https://openalex.org/W2021919788","https://openalex.org/W2024455558","https://openalex.org/W2028263411","https://openalex.org/W2035266068","https://openalex.org/W2035687084","https://openalex.org/W2035738941","https://openalex.org/W2040333447","https://openalex.org/W2049015709","https://openalex.org/W2056230513","https://openalex.org/W2056511887","https://openalex.org/W2057477511","https://openalex.org/W2060469824","https://openalex.org/W2067901141","https://openalex.org/W2069768395","https://openalex.org/W2074718022","https://openalex.org/W2079995754","https://openalex.org/W2083519984","https://openalex.org/W2092915328","https://openalex.org/W2096048289","https://openalex.org/W2102377211","https://openalex.org/W2112005274","https://openalex.org/W2115523483","https://openalex.org/W2128572087","https://openalex.org/W2136729627","https://openalex.org/W2139776307","https://openalex.org/W2160544821","https://openalex.org/W2162296614","https://openalex.org/W2327962932","https://openalex.org/W2337120805","https://openalex.org/W2364475390","https://openalex.org/W2593641252","https://openalex.org/W2594024553","https://openalex.org/W2801036213","https://openalex.org/W2883878245","https://openalex.org/W2907627192","https://openalex.org/W2944511810","https://openalex.org/W2951742280","https://openalex.org/W3014790073","https://openalex.org/W3039385523","https://openalex.org/W3095125339","https://openalex.org/W3120898108","https://openalex.org/W3141159078","https://openalex.org/W3156401343","https://openalex.org/W3201539868","https://openalex.org/W3209375464","https://openalex.org/W3209554085","https://openalex.org/W4205578619","https://openalex.org/W4206793140","https://openalex.org/W4280609891","https://openalex.org/W4281786804","https://openalex.org/W4283325670","https://openalex.org/W4290672950","https://openalex.org/W4295532582","https://openalex.org/W4296766525","https://openalex.org/W4313478099","https://openalex.org/W4366829684","https://openalex.org/W4367049415","https://openalex.org/W4379599100","https://openalex.org/W4381481308","https://openalex.org/W4382011902","https://openalex.org/W4384933616","https://openalex.org/W4386337354","https://openalex.org/W4387363921","https://openalex.org/W4387931208","https://openalex.org/W4387951124","https://openalex.org/W4394933376","https://openalex.org/W4396721167","https://openalex.org/W4405514994"],"related_works":["https://openalex.org/W7148890693","https://openalex.org/W4415242526","https://openalex.org/W2894823011","https://openalex.org/W4295532582","https://openalex.org/W2586477885","https://openalex.org/W3000632182","https://openalex.org/W2364475390","https://openalex.org/W2990262863","https://openalex.org/W7154069484","https://openalex.org/W4404540413"],"abstract_inverted_index":{"Aptamers,":[0],"functional":[1],"nucleic":[2,204],"acids":[3],"recognized":[4],"for":[5,60,66,100,117,123,146],"their":[6],"high":[7],"target-binding":[8],"affinity":[9,116,145],"and":[10,19,38,50,70,128,139,202],"specificity,":[11,172],"have":[12],"been":[13],"extensively":[14],"employed":[15,89],"in":[16,74,159,190],"biosensors,":[17],"diagnostics,":[18],"therapeutics.":[20],"Conventional":[21],"screening":[22],"methods":[23],"apply":[24],"evolutionary":[25],"pressure":[26],"to":[27,34,47,96,133,169],"optimize":[28],"affinity,":[29],"while":[30,126],"counter-selections":[31],"are":[32],"used":[33],"minimize":[35],"off-target":[36],"binding":[37],"improve":[39],"specificity.":[40],"However,":[41],"aptamer":[42,68,111,151,171,193],"specificity":[43,73],"characterization":[44],"remains":[45],"limited":[46],"target":[48,72],"analogs":[49],"experimental":[51,83],"controls.":[52],"A":[53,149],"systematic":[54],"exploration":[55],"of":[56,82,177,186,199],"the":[57,80,108,118,147,167,175,184,197],"chemical":[58],"space":[59],"aptamer-binding":[61,200],"chemicals":[62],"(targets)":[63],"is":[64],"crucial":[65],"uncovering":[67],"versatility":[69,201],"enhancing":[71],"practical":[75],"applications,":[76],"a":[77,90,113,156],"task":[78],"beyond":[79],"scope":[81],"approaches.":[84],"To":[85],"address":[86],"this,":[87],"we":[88],"high-throughput":[91],"three-stage":[92],"structure-based":[93],"computational":[94,188],"framework":[95,189],"identify":[97],"potent":[98,192],"binders":[99],"two":[101],"model":[102],"aptamers.":[103],"Our":[104],"findings":[105,182],"revealed":[106],"that":[107],"l-argininamide":[109],"(L-Arm)-binding":[110],"has":[112],"31-fold":[114],"higher":[115],"retromer":[119],"chaperone":[120],"R55":[121],"than":[122,153],"L-Arm":[124,178],"itself,":[125],"guanethidine":[127],"ZINC10314005":[129],"exhibited":[130],"comparable":[131],"affinities":[132],"L-Arm.":[134],"In":[135],"another":[136],"case,":[137],"norfloxacin":[138],"difloxacin":[140],"demonstrated":[141],"over":[142],"10-fold":[143],"greater":[144],"ochratoxin":[148],"(OTA)-binding":[150],"OBA3":[152],"OTA,":[154],"introducing":[155],"fresh":[157],"paradigm":[158],"aptamer-target":[160],"interactions.":[161],"Furthermore,":[162],"pocket":[163],"mutation":[164],"studies":[165],"highlighted":[166],"potential":[168],"tune":[170],"significantly":[173],"impacting":[174],"bindings":[176],"or":[179],"norfloxacin.":[180],"These":[181],"demonstrate":[183],"effectiveness":[185],"our":[187],"discovering":[191],"binders,":[194],"thereby":[195],"expanding":[196],"understanding":[198],"advancing":[203],"acid-targeted":[205],"drug":[206],"discovery.":[207]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2025-03-04T00:00:00"}
