{"id":"https://openalex.org/W4413112789","doi":"https://doi.org/10.1093/bib/bbae531","title":"Deep reinforcement learning as an interaction agent to steer fragment-based 3D molecular generation for protein pockets","display_name":"Deep reinforcement learning as an interaction agent to steer fragment-based 3D molecular generation for protein pockets","publication_year":2024,"publication_date":"2024-11-02","ids":{"openalex":"https://openalex.org/W4413112789","doi":"https://doi.org/10.1093/bib/bbae531","pmid":"https://pubmed.ncbi.nlm.nih.gov/40794942"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae531","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae531","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbae531/63959033/bbae531.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/bbae531/63959033/bbae531.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100441849","display_name":"Xudong Zhang","orcid":"https://orcid.org/0000-0002-3943-1428"},"institutions":[{"id":"https://openalex.org/I4210153623","display_name":"Shanghai First Maternity and Infant Hospital","ror":"https://ror.org/05myyzn85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210153623"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xudong Zhang","raw_affiliation_strings":["Shanghai Key Laboratory of Maternal Fetal Medicine , Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Computer Science and Technology, Tongji University, Shanghai 200092,","Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Computer Science and Technology, Tongji University, Shanghai 200092, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Key Laboratory of Maternal Fetal Medicine , Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Computer Science and Technology, Tongji University, Shanghai 200092,","institution_ids":["https://openalex.org/I4210153623"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Computer Science and Technology, Tongji University, Shanghai 200092, China","institution_ids":["https://openalex.org/I4210153623"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091579598","display_name":"Jing Hou","orcid":"https://orcid.org/0000-0003-4778-137X"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Hou","raw_affiliation_strings":["School of Computer Science and Technology , Tongji University, Shanghai 200092,","School of Computer Science and Technology, Tongji University, Shanghai 200092, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology , Tongji University, Shanghai 200092,","institution_ids":["https://openalex.org/I116953780"]},{"raw_affiliation_string":"School of Computer Science and Technology, Tongji University, Shanghai 200092, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070358967","display_name":"Sanqing Qu","orcid":"https://orcid.org/0009-0000-0377-7120"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sanqing Qu","raw_affiliation_strings":["School of Computer Science and Technology , Tongji University, Shanghai 200092,","School of Computer Science and Technology, Tongji University, Shanghai 200092, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology , Tongji University, Shanghai 200092,","institution_ids":["https://openalex.org/I116953780"]},{"raw_affiliation_string":"School of Computer Science and Technology, Tongji University, Shanghai 200092, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038013125","display_name":"Fan L\u00fc","orcid":"https://orcid.org/0000-0002-8496-3941"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fan Lu","raw_affiliation_strings":["School of Computer Science and Technology , Tongji University, Shanghai 200092,","School of Computer Science and Technology, Tongji University, Shanghai 200092, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology , Tongji University, Shanghai 200092,","institution_ids":["https://openalex.org/I116953780"]},{"raw_affiliation_string":"School of Computer Science and Technology, Tongji University, Shanghai 200092, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042231897","display_name":"Zhixin Tian","orcid":"https://orcid.org/0000-0002-2877-8282"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhixin Tian","raw_affiliation_strings":["School of Chemical Science and Engineering , Tongji University, Shanghai 200092,","School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Chemical Science and Engineering , Tongji University, Shanghai 200092,","institution_ids":["https://openalex.org/I116953780"]},{"raw_affiliation_string":"School of Chemical Science and Engineering, Tongji University, Shanghai 200092, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063781430","display_name":"Alois Knoll","orcid":"https://orcid.org/0000-0003-4840-076X"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alois Knoll","raw_affiliation_strings":["School of Computation , Information and Technology, Technical University of Munich, 85748, Garching b. M\u00fcnchen","School of Computation, Information and Technology, Technical University of Munich, 85748, Garching b. M\u00fcnchen"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computation , Information and Technology, Technical University of Munich, 85748, Garching b. M\u00fcnchen","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"School of Computation, Information and Technology, Technical University of Munich, 85748, Garching b. M\u00fcnchen","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101684449","display_name":"Guang Chen","orcid":"https://orcid.org/0000-0001-6644-9618"},"institutions":[{"id":"https://openalex.org/I116953780","display_name":"Tongji University","ror":"https://ror.org/03rc6as71","country_code":"CN","type":"education","lineage":["https://openalex.org/I116953780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guang Chen","raw_affiliation_strings":["School of Computer Science and Technology , Tongji University, Shanghai 200092,","School of Computer Science and Technology, Tongji University, Shanghai 200092, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology , Tongji University, Shanghai 200092,","institution_ids":["https://openalex.org/I116953780"]},{"raw_affiliation_string":"School of Computer Science and Technology, Tongji University, Shanghai 200092, China","institution_ids":["https://openalex.org/I116953780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058603003","display_name":"Shaorong Gao","orcid":"https://orcid.org/0000-0003-1041-3928"},"institutions":[{"id":"https://openalex.org/I4210153623","display_name":"Shanghai First Maternity and Infant Hospital","ror":"https://ror.org/05myyzn85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210153623"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaorong Gao","raw_affiliation_strings":["Shanghai Key Laboratory of Maternal Fetal Medicine , Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092,","Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Key Laboratory of Maternal Fetal Medicine , Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092,","institution_ids":["https://openalex.org/I4210153623"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China","institution_ids":["https://openalex.org/I4210153623"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100430699","display_name":"Yanping Zhang","orcid":"https://orcid.org/0000-0001-8150-7265"},"institutions":[{"id":"https://openalex.org/I4210153623","display_name":"Shanghai First Maternity and Infant Hospital","ror":"https://ror.org/05myyzn85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210153623"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanping Zhang","raw_affiliation_strings":["Shanghai Key Laboratory of Maternal Fetal Medicine , Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092,","Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Key Laboratory of Maternal Fetal Medicine , Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092,","institution_ids":["https://openalex.org/I4210153623"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China","institution_ids":["https://openalex.org/I4210153623"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5100441849"],"corresponding_institution_ids":["https://openalex.org/I4210153623"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.3776,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.69304772,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9821000099182129,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9821000099182129,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9761000275611877,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.9682000279426575,"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/fragment","display_name":"Fragment (logic)","score":0.856249213218689},{"id":"https://openalex.org/keywords/reinforcement-learning","display_name":"Reinforcement learning","score":0.6768350005149841},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5517180562019348},{"id":"https://openalex.org/keywords/reinforcement","display_name":"Reinforcement","score":0.5388211011886597},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.508873701095581},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.17035749554634094},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.09819942712783813}],"concepts":[{"id":"https://openalex.org/C2776235265","wikidata":"https://www.wikidata.org/wiki/Q18392052","display_name":"Fragment (logic)","level":2,"score":0.856249213218689},{"id":"https://openalex.org/C97541855","wikidata":"https://www.wikidata.org/wiki/Q830687","display_name":"Reinforcement learning","level":2,"score":0.6768350005149841},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5517180562019348},{"id":"https://openalex.org/C67203356","wikidata":"https://www.wikidata.org/wiki/Q1321905","display_name":"Reinforcement","level":2,"score":0.5388211011886597},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.508873701095581},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.17035749554634094},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.09819942712783813},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098408","descriptor_name":"Reinforcement Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098408","descriptor_name":"Reinforcement Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098408","descriptor_name":"Reinforcement Machine Learning","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":"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae531","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae531","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbae531/63959033/bbae531.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:40794942","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40794942","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:12718310","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12718310/","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/bbae531","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae531","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbae531/63959033/bbae531.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/G1423305676","display_name":null,"funder_award_id":"92168205","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1845911978","display_name":null,"funder_award_id":"2022YFA1103102","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G3046883789","display_name":null,"funder_award_id":"32370616","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4530127105","display_name":null,"funder_award_id":"945539","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G5120449483","display_name":null,"funder_award_id":"32170589","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G793942182","display_name":null,"funder_award_id":"22074105","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8767435255","display_name":null,"funder_award_id":"945539","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"},{"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/W4413112789.pdf"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1970651561","https://openalex.org/W1975447903","https://openalex.org/W1981737096","https://openalex.org/W1986240377","https://openalex.org/W1998848097","https://openalex.org/W2022476850","https://openalex.org/W2025816743","https://openalex.org/W2030971064","https://openalex.org/W2038542598","https://openalex.org/W2046376809","https://openalex.org/W2047509756","https://openalex.org/W2071791280","https://openalex.org/W2074978477","https://openalex.org/W2108389384","https://openalex.org/W2134967712","https://openalex.org/W2151697120","https://openalex.org/W2164088236","https://openalex.org/W2244785476","https://openalex.org/W2529996553","https://openalex.org/W2578240541","https://openalex.org/W2950954328","https://openalex.org/W2999044305","https://openalex.org/W3008588639","https://openalex.org/W3080588469","https://openalex.org/W3082081167","https://openalex.org/W3082411326","https://openalex.org/W3116865743","https://openalex.org/W3194855384","https://openalex.org/W3200806939","https://openalex.org/W3201249640","https://openalex.org/W3209056694","https://openalex.org/W3209764902","https://openalex.org/W3212070798","https://openalex.org/W4200150297","https://openalex.org/W4206367183","https://openalex.org/W4214868967","https://openalex.org/W4248107770","https://openalex.org/W4282913408","https://openalex.org/W4296184108","https://openalex.org/W4309908854","https://openalex.org/W4313703391","https://openalex.org/W4313816476","https://openalex.org/W4321769975","https://openalex.org/W4386498912"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W1973480752","https://openalex.org/W2805502594","https://openalex.org/W3132641048","https://openalex.org/W4403688099","https://openalex.org/W4253208712","https://openalex.org/W31439402","https://openalex.org/W2217679042"],"abstract_inverted_index":{"Designing":[0],"high-affinity":[1],"molecules":[2],"for":[3,41,48,108,192],"protein":[4,8,36,81],"targets":[5],"(especially":[6],"novel":[7],"families)":[9],"is":[10,84],"a":[11,60,68,87,103,114,128],"crucial":[12],"yet":[13],"challenging":[14],"task":[15],"in":[16,25,160],"drug":[17],"discovery.":[18],"Recently,":[19],"there":[20],"has":[21],"been":[22],"tremendous":[23],"progress":[24],"structure-based":[26,194],"3D":[27,77,178],"molecular":[28,42,78,179],"generative":[29],"models":[30],"that":[31,62,153],"incorporate":[32],"structural":[33],"information":[34],"of":[35,105,131,147,174],"pockets.":[37,82],"However,":[38],"the":[39,46,97,138,142,172],"capacity":[40],"representation":[43],"learning":[44,66],"and":[45,94,110,134,145,182],"generalization":[47,124],"capturing":[49,177],"interaction":[50,70,92,183],"patterns":[51,184],"need":[52],"substantial":[53],"further":[54],"developments.":[55],"Here,":[56],"we":[57],"propose":[58],"AMG,":[59],"framework":[61,100],"leverages":[63],"deep":[64],"reinforcement":[65],"as":[67],"pocket-ligand":[69,186],"agent":[71],"(IA)":[72],"to":[73,90,121],"gradually":[74],"steer":[75],"fragment-based":[76],"generation":[79],"targeting":[80],"AMG":[83,120,154,175],"trained":[85],"using":[86],"two-stage":[88],"strategy":[89],"capture":[91],"features":[93,181],"explicitly":[95],"optimize":[96],"IA.":[98],"The":[99],"also":[101],"introduces":[102],"pair":[104],"separate":[106],"encoders":[107],"pockets":[109,133],"ligands,":[111],"coupled":[112],"with":[113],"dedicated":[115],"pre-training":[116],"strategy.":[117],"This":[118],"enables":[119],"enhance":[122],"its":[123,189],"ability":[125],"by":[126,141],"leveraging":[127],"vast":[129],"repository":[130],"undocked":[132],"molecules,":[135],"thus":[136],"mitigating":[137],"constraints":[139],"posed":[140],"limited":[143],"quantity":[144],"quality":[146],"available":[148],"datasets.":[149],"Extensive":[150],"evaluations":[151],"demonstrate":[152],"significantly":[155],"outperforms":[156],"five":[157],"state-of-the-art":[158],"baselines":[159],"affinity":[161],"performance":[162],"while":[163],"maintaining":[164],"proper":[165],"drug-likeness":[166],"properties.":[167],"Furthermore,":[168],"visual":[169],"analysis":[170],"confirms":[171],"superiority":[173],"at":[176],"geometrical":[180],"within":[185],"complexes,":[187],"indicating":[188],"considerable":[190],"promise":[191],"various":[193],"downstream":[195],"tasks.":[196]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-23T08:51:43.019350","created_date":"2025-10-10T00:00:00"}
