{"id":"https://openalex.org/W4412488438","doi":"https://doi.org/10.1093/bib/bbaf345","title":"A 3D pocket-aware lead optimization model with knowledge guidance and its application for discovery of new glutaminyl cyclase inhibitors","display_name":"A 3D pocket-aware lead optimization model with knowledge guidance and its application for discovery of new glutaminyl cyclase inhibitors","publication_year":2025,"publication_date":"2025-06-27","ids":{"openalex":"https://openalex.org/W4412488438","doi":"https://doi.org/10.1093/bib/bbaf345","pmid":"https://pubmed.ncbi.nlm.nih.gov/40669838"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf345","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf345","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf345/63779640/bbaf345.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in 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/bib/article-pdf/26/4/bbaf345/63779640/bbaf345.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Anjie Qiao","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Anjie Qiao","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100436577","display_name":"Yuting Chen","orcid":"https://orcid.org/0000-0003-4579-6498"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuting Chen","raw_affiliation_strings":["West China School of Pharmacy, Sichuan University , No. 17 Southern Renmin Road, Chengdu 610041 , Sichuan,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"West China School of Pharmacy, Sichuan University , No. 17 Southern Renmin Road, Chengdu 610041 , Sichuan,","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101562927","display_name":"Junjie Xie","orcid":"https://orcid.org/0009-0008-9927-0452"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junjie Xie","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062664714","display_name":"Weifeng Huang","orcid":"https://orcid.org/0009-0006-9335-3877"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weifeng Huang","raw_affiliation_strings":["School of Pharmaceutical Science, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","School of Pharmaceutical Science, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Science, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Pharmaceutical Science, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100396796","display_name":"Hao Zhang","orcid":"https://orcid.org/0000-0001-6774-941X"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Zhang","raw_affiliation_strings":["School of Pharmaceutical Science, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","School of Pharmaceutical Science, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Science, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Pharmaceutical Science, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113328134","display_name":"Qirui Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qirui Deng","raw_affiliation_strings":["School of Pharmaceutical Science, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","School of Pharmaceutical Science, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Science, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Pharmaceutical Science, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015329746","display_name":"Jiahua Rao","orcid":"https://orcid.org/0000-0002-6840-8198"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiahua Rao","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100938246","display_name":"Ji Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ji Deng","raw_affiliation_strings":["West China School of Pharmacy, Sichuan University , No. 17 Southern Renmin Road, Chengdu 610041 , Sichuan,","West China School of Pharmacy, Sichuan University, No. 17 Southern Renmin Road, Chengdu 610041, Sichuan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"West China School of Pharmacy, Sichuan University , No. 17 Southern Renmin Road, Chengdu 610041 , Sichuan,","institution_ids":["https://openalex.org/I24185976"]},{"raw_affiliation_string":"West China School of Pharmacy, Sichuan University, No. 17 Southern Renmin Road, Chengdu 610041, Sichuan, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101152813","display_name":"Fanbo Meng","orcid":"https://orcid.org/0009-0006-1717-9037"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fanbo Meng","raw_affiliation_strings":["West China School of Pharmacy, Sichuan University , No. 17 Southern Renmin Road, Chengdu 610041 , Sichuan,","West China School of Pharmacy, Sichuan University, No. 17 Southern Renmin Road, Chengdu 610041, Sichuan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"West China School of Pharmacy, Sichuan University , No. 17 Southern Renmin Road, Chengdu 610041 , Sichuan,","institution_ids":["https://openalex.org/I24185976"]},{"raw_affiliation_string":"West China School of Pharmacy, Sichuan University, No. 17 Southern Renmin Road, Chengdu 610041, Sichuan, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100422431","display_name":"Zhen Wang","orcid":"https://orcid.org/0000-0003-4002-7892"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Wang","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016050256","display_name":"Mingyuan Xu","orcid":"https://orcid.org/0000-0003-0463-4249"},"institutions":[{"id":"https://openalex.org/I4210090512","display_name":"Guangzhou Experimental Station","ror":"https://ror.org/00f2c2516","country_code":"CN","type":"facility","lineage":["https://openalex.org/I107851509","https://openalex.org/I4210090512","https://openalex.org/I4210127390","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingyuan Xu","raw_affiliation_strings":["Guangzhou National Laboratory , No. 9 XinDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005 , Guangdong,","Guangzhou National Laboratory, No. 9 XinDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong, China"],"raw_orcid":"https://orcid.org/0000-0003-0463-4249","affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory , No. 9 XinDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005 , Guangdong,","institution_ids":["https://openalex.org/I4210090512"]},{"raw_affiliation_string":"Guangzhou National Laboratory, No. 9 XinDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong, China","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100729956","display_name":"Hongming Chen","orcid":"https://orcid.org/0000-0002-8065-8333"},"institutions":[{"id":"https://openalex.org/I4210090512","display_name":"Guangzhou Experimental Station","ror":"https://ror.org/00f2c2516","country_code":"CN","type":"facility","lineage":["https://openalex.org/I107851509","https://openalex.org/I4210090512","https://openalex.org/I4210127390","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongming Chen","raw_affiliation_strings":["Guangzhou National Laboratory , No. 9 XinDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005 , Guangdong,","Guangzhou National Laboratory, No. 9 XinDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory , No. 9 XinDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005 , Guangdong,","institution_ids":["https://openalex.org/I4210090512"]},{"raw_affiliation_string":"Guangzhou National Laboratory, No. 9 XinDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong, China","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043459237","display_name":"Jiancong Xie","orcid":"https://orcid.org/0000-0001-9030-0709"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiancong Xie","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China"],"raw_orcid":"https://orcid.org/0000-0001-9030-0709","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075817762","display_name":"Shuangjia Zheng","orcid":"https://orcid.org/0000-0001-9747-4285"},"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":"Shuangjia Zheng","raw_affiliation_strings":["Global Institute of Future Technology, No. 800 Dongchuan Road, Shanghai Jiao Tong University , Shanghai 200240 ,","Global Institute of Future Technology, No. 800 Dongchuan Road, Shanghai Jiao Tong University, Shanghai 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Global Institute of Future Technology, No. 800 Dongchuan Road, Shanghai Jiao Tong University , Shanghai 200240 ,","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Global Institute of Future Technology, No. 800 Dongchuan Road, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023539493","display_name":"Yuedong Yang","orcid":"https://orcid.org/0000-0002-6782-2813"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuedong Yang","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China"],"raw_orcid":"https://orcid.org/0000-0002-6782-2813","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031861128","display_name":"Guo\u2010Bo Li","orcid":"https://orcid.org/0000-0002-4915-6677"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guo-Bo Li","raw_affiliation_strings":["West China School of Pharmacy, Sichuan University , No. 17 Southern Renmin Road, Chengdu 610041 , Sichuan,","West China School of Pharmacy, Sichuan University, No. 17 Southern Renmin Road, Chengdu 610041, Sichuan, China"],"raw_orcid":"https://orcid.org/0000-0002-4915-6677","affiliations":[{"raw_affiliation_string":"West China School of Pharmacy, Sichuan University , No. 17 Southern Renmin Road, Chengdu 610041 , Sichuan,","institution_ids":["https://openalex.org/I24185976"]},{"raw_affiliation_string":"West China School of Pharmacy, Sichuan University, No. 17 Southern Renmin Road, Chengdu 610041, Sichuan, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005501007","display_name":"Jinping Lei","orcid":"https://orcid.org/0000-0002-6888-2973"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinping Lei","raw_affiliation_strings":["School of Pharmaceutical Science, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","School of Pharmaceutical Science, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China"],"raw_orcid":"https://orcid.org/0000-0002-6888-2973","affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Science, Sun Yat-sen University , No. 132 Waihuan East Road, Guangzhou 510006 , Guangdong,","institution_ids":["https://openalex.org/I157773358"]},{"raw_affiliation_string":"School of Pharmaceutical Science, Sun Yat-sen University, No. 132 Waihuan East Road, Guangzhou 510006, Guangdong, China","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":17,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I157773358"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.9771,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.94110899,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"26","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9969000220298767,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9957000017166138,"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/drug-discovery","display_name":"Drug discovery","score":0.6419508457183838},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5434548854827881},{"id":"https://openalex.org/keywords/lead","display_name":"Lead (geology)","score":0.4956260919570923},{"id":"https://openalex.org/keywords/rational-design","display_name":"Rational design","score":0.42952239513397217},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4145069718360901},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3659139573574066},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.36114054918289185},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.20051687955856323},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.19213417172431946},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1403648853302002},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1242036521434784}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.6419508457183838},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5434548854827881},{"id":"https://openalex.org/C2777093003","wikidata":"https://www.wikidata.org/wiki/Q6508345","display_name":"Lead (geology)","level":2,"score":0.4956260919570923},{"id":"https://openalex.org/C53105671","wikidata":"https://www.wikidata.org/wiki/Q14777816","display_name":"Rational design","level":2,"score":0.42952239513397217},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4145069718360901},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3659139573574066},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.36114054918289185},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.20051687955856323},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.19213417172431946},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1403648853302002},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1242036521434784},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004791","descriptor_name":"Enzyme Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":true},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019881","descriptor_name":"Aminoacyltransferases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf345","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf345","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf345/63779640/bbaf345.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40669838","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40669838","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12266789","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12266789","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf345","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf345","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf345/63779640/bbaf345.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4206303254","display_name":null,"funder_award_id":"62402314","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6446954825","display_name":null,"funder_award_id":"2023YFF1204901","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G658642563","display_name":null,"funder_award_id":"82122065","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7301097705","display_name":null,"funder_award_id":"82473845","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7771303265","display_name":null,"funder_award_id":"2023YFF1204900","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8143382980","display_name":null,"funder_award_id":"2023YFF1204902","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/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4412488438.pdf"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W2024656644","https://openalex.org/W2028938218","https://openalex.org/W2114162221","https://openalex.org/W2120864201","https://openalex.org/W2944973540","https://openalex.org/W2956961449","https://openalex.org/W2971690404","https://openalex.org/W3006759222","https://openalex.org/W3082411326","https://openalex.org/W3096418018","https://openalex.org/W3100358278","https://openalex.org/W3107514001","https://openalex.org/W3138705992","https://openalex.org/W3161725201","https://openalex.org/W3164973443","https://openalex.org/W3168436232","https://openalex.org/W3198869316","https://openalex.org/W3212417448","https://openalex.org/W3213530673","https://openalex.org/W4221138292","https://openalex.org/W4224311800","https://openalex.org/W4225637038","https://openalex.org/W4280535976","https://openalex.org/W4281701642","https://openalex.org/W4296128995","https://openalex.org/W4306728530","https://openalex.org/W4309447026","https://openalex.org/W4317436054","https://openalex.org/W4323256092","https://openalex.org/W4387334953","https://openalex.org/W4389257854","https://openalex.org/W4391023360","https://openalex.org/W4391187294","https://openalex.org/W4392015344","https://openalex.org/W4392822048","https://openalex.org/W4394718179","https://openalex.org/W4399238399","https://openalex.org/W4403610674","https://openalex.org/W4404074819","https://openalex.org/W4405153032","https://openalex.org/W4407789339","https://openalex.org/W4408194530","https://openalex.org/W4408328169","https://openalex.org/W6804214328","https://openalex.org/W6810653082","https://openalex.org/W6838000958","https://openalex.org/W6838191877","https://openalex.org/W6862998299"],"related_works":["https://openalex.org/W4255463199","https://openalex.org/W4281691423","https://openalex.org/W2411039299","https://openalex.org/W2013003323","https://openalex.org/W1981076832","https://openalex.org/W2063700634","https://openalex.org/W2024773645","https://openalex.org/W2001717001","https://openalex.org/W2043147644","https://openalex.org/W2189969113"],"abstract_inverted_index":{"Lead":[0],"optimization,":[1],"aimed":[2],"at":[3],"improving":[4],"binding":[5,65,83,122,151],"affinity":[6,66,84,123,148],"or":[7],"other":[8],"properties":[9],"of":[10,32,63,104,120,199],"hit":[11],"compounds,":[12],"is":[13,92,115,125],"a":[14,51],"crucial":[15],"task":[16],"in":[17,28,111],"drug":[18,35],"discovery.":[19],"Though":[20],"deep":[21],"learning-based":[22],"3D":[23,52],"generative":[24],"models":[25,142],"showed":[26],"promise":[27],"enhancing":[29],"the":[30,61,74,89,102,118,121,191],"efficiency":[31],"de":[33],"novo":[34],"design":[36],"recently,":[37],"less":[38],"research":[39],"and":[40,67,85,101,108,149,153,202],"attention":[41],"has":[42],"garnered":[43],"for":[44,78],"structure-based":[45],"lead":[46,79,144,173],"optimization.":[47],"Herein,":[48],"we":[49],"propose":[50],"pocket-aware":[53],"diffusion":[54,95],"model":[55],"named":[56],"Diffleop,":[57],"which":[58],"explicitly":[59],"incorporates":[60],"knowledge":[62],"protein-ligand":[64],"information":[68],"on":[69,96,143],"covalent":[70],"bonds":[71],"to":[72,167],"guide":[73],"denoising":[75],"sampling":[76,113],"process":[77],"optimization":[80,145],"with":[81,129,146,159,190],"enhanced":[82],"rational":[86,161],"properties.":[87],"Specifically,":[88],"bond":[90,109],"constraint":[91],"achieved":[93],"through":[94,127],"fully":[97],"connected":[98],"molecular":[99],"graphs,":[100],"determination":[103],"atom":[105,107],"positions,":[106],"types":[110],"each":[112],"step":[114],"guided":[116],"by":[117],"gradient":[119],"that":[124,138],"predicted":[126],"fitting":[128],"an":[130,196],"E(3)-equivariant":[131],"expert":[132],"network.":[133],"The":[134],"comprehensive":[135],"evaluations":[136],"indicated":[137],"Diffleop":[139,163],"outperforms":[140],"baseline":[141],"higher":[147],"more":[150,156,160],"interactions,":[152],"can":[154],"generate":[155],"drug-like":[157],"molecules":[158],"structures.":[162],"was":[164],"further":[165],"applied":[166],"optimize":[168],"5-methyl-1H-imidazole,":[169],"our":[170],"newly":[171],"discovered":[172],"compound":[174],"targeting":[175],"human":[176],"glutaminyl":[177],"cyclases":[178],"(QCs).":[179],"Three":[180],"synthesized":[181],"compounds":[182],"exhibit":[183],"substantially":[184],"improved":[185],"inhibitory":[186],"activities":[187],"against":[188],"QCs,":[189],"most":[192],"effective":[193],"one":[194],"showing":[195],"IC50":[197],"value":[198],"8":[200],"nM":[201],"3.5-fold":[203],"better":[204],"than":[205],"clinical":[206],"candidate":[207],"PQ912.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2025-12-23T23:11:35.936235","created_date":"2025-10-10T00:00:00"}
