{"id":"https://openalex.org/W4415220428","doi":"https://doi.org/10.1093/bib/bbaf542","title":"Designing high-affinity 3D drug molecules via geometric spatial perception diffusion model","display_name":"Designing high-affinity 3D drug molecules via geometric spatial perception diffusion model","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4415220428","doi":"https://doi.org/10.1093/bib/bbaf542","pmid":"https://pubmed.ncbi.nlm.nih.gov/41092059"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf542","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf542","pdf_url":null,"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":null,"license_id":null,"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://doi.org/10.1093/bib/bbaf542","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103072612","display_name":"Hao Lu","orcid":"https://orcid.org/0009-0009-6553-6205"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Lu","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,"],"raw_orcid":"https://orcid.org/0009-0009-6553-6205","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101905330","display_name":"Zhiqiang Wei","orcid":"https://orcid.org/0000-0002-2774-3168"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiqiang Wei","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100440970","display_name":"Jiaming Liu","orcid":"https://orcid.org/0000-0002-1042-4443"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaming Liu","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jiangrui Li","orcid":null},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiangrui Li","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115596389","display_name":"Qian Wang","orcid":"https://orcid.org/0009-0006-7421-1451"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qian Wang","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,","institution_ids":["https://openalex.org/I59028903"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100458827","display_name":"Hao Liu","orcid":"https://orcid.org/0000-0002-6572-3408"},"institutions":[{"id":"https://openalex.org/I59028903","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186","country_code":"CN","type":"education","lineage":["https://openalex.org/I59028903"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Liu","raw_affiliation_strings":["College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Ocean University of China , Songling Road, 266100 Shandong Province ,","institution_ids":["https://openalex.org/I59028903"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I59028903"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.6561,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.91763921,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"26","issue":"5","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":0.9997000098228455,"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":0.9997000098228455,"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":0.9965999722480774,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9606999754905701,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5619000196456909},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5009999871253967},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.49129998683929443},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.4526999890804291},{"id":"https://openalex.org/keywords/molecular-binding","display_name":"Molecular binding","score":0.40720000863075256},{"id":"https://openalex.org/keywords/perception","display_name":"Perception","score":0.39750000834465027},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.38589999079704285},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.3686999976634979},{"id":"https://openalex.org/keywords/molecular-recognition","display_name":"Molecular recognition","score":0.34610000252723694}],"concepts":[{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5619000196456909},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5562000274658203},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5009999871253967},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.49129998683929443},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.4526999890804291},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4271000027656555},{"id":"https://openalex.org/C2777735830","wikidata":"https://www.wikidata.org/wiki/Q6507061","display_name":"Molecular binding","level":3,"score":0.40720000863075256},{"id":"https://openalex.org/C26760741","wikidata":"https://www.wikidata.org/wiki/Q160402","display_name":"Perception","level":2,"score":0.39750000834465027},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.38589999079704285},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3686999976634979},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36570000648498535},{"id":"https://openalex.org/C179303850","wikidata":"https://www.wikidata.org/wiki/Q4300362","display_name":"Molecular recognition","level":3,"score":0.34610000252723694},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.34150001406669617},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.3276999890804291},{"id":"https://openalex.org/C198082294","wikidata":"https://www.wikidata.org/wiki/Q3399648","display_name":"Position (finance)","level":2,"score":0.32170000672340393},{"id":"https://openalex.org/C2779767902","wikidata":"https://www.wikidata.org/wiki/Q17037278","display_name":"Molecular communication","level":4,"score":0.3059999942779541},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3021000027656555},{"id":"https://openalex.org/C129782007","wikidata":"https://www.wikidata.org/wiki/Q162886","display_name":"Euclidean geometry","level":2,"score":0.2858999967575073},{"id":"https://openalex.org/C120174047","wikidata":"https://www.wikidata.org/wiki/Q847073","display_name":"Euclidean distance","level":2,"score":0.28529998660087585},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.28060001134872437},{"id":"https://openalex.org/C178910836","wikidata":"https://www.wikidata.org/wiki/Q2196961","display_name":"Molecular model","level":2,"score":0.2782000005245209},{"id":"https://openalex.org/C164923092","wikidata":"https://www.wikidata.org/wiki/Q3705921","display_name":"Molecular descriptor","level":3,"score":0.26980000734329224},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.26969999074935913},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.26809999346733093},{"id":"https://openalex.org/C3019007443","wikidata":"https://www.wikidata.org/wiki/Q568742","display_name":"3d model","level":2,"score":0.25290000438690186},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.25200000405311584}],"mesh":[{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004058","descriptor_name":"Diffusion","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":"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf542","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf542","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41092059","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41092059","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:europepmc.org:11331666","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12526910","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf542","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf542","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322440","display_name":"Ocean University of China","ror":"https://ror.org/04rdtx186"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W2074473216","https://openalex.org/W2092285329","https://openalex.org/W2560674852","https://openalex.org/W2950954328","https://openalex.org/W2962834855","https://openalex.org/W3027325047","https://openalex.org/W3082411326","https://openalex.org/W3135156311","https://openalex.org/W3168436232","https://openalex.org/W3177828909","https://openalex.org/W4213451219","https://openalex.org/W4221138292","https://openalex.org/W4221149947","https://openalex.org/W4281781228","https://openalex.org/W4295180193","https://openalex.org/W4309047034","https://openalex.org/W4367049415","https://openalex.org/W4368357923","https://openalex.org/W4382239902","https://openalex.org/W4385343013","https://openalex.org/W4385454156","https://openalex.org/W4386804497","https://openalex.org/W4387195417","https://openalex.org/W4387378779","https://openalex.org/W4387451313","https://openalex.org/W4388185854","https://openalex.org/W4389257854","https://openalex.org/W4391932789","https://openalex.org/W4392596618","https://openalex.org/W4392653998","https://openalex.org/W4392822048","https://openalex.org/W4393111365","https://openalex.org/W4393153201","https://openalex.org/W4393181728","https://openalex.org/W4393222489","https://openalex.org/W4393967802","https://openalex.org/W4394718179","https://openalex.org/W4396721167","https://openalex.org/W4396789292","https://openalex.org/W4399781535","https://openalex.org/W4399836196","https://openalex.org/W4400037855","https://openalex.org/W4401102983","https://openalex.org/W4402887448","https://openalex.org/W4404105372","https://openalex.org/W4404610749","https://openalex.org/W4404826794","https://openalex.org/W4405194591","https://openalex.org/W4407789339","https://openalex.org/W4410827740"],"related_works":[],"abstract_inverted_index":{"Designing":[0],"high-affinity":[1],"molecules":[2,21,129,150],"for":[3,12],"certain":[4],"proteins":[5,23],"is":[6],"a":[7,50,79,136],"fundamental":[8],"and":[9,22,71,118,151],"challenging":[10],"problem":[11],"drug":[13,149],"discovery,":[14],"particularly":[15],"when":[16],"considering":[17],"atomic":[18],"interactions":[19,146],"between":[20,147],"in":[24,45,126,142],"3D":[25,28,148],"space.":[26,47],"Current":[27],"molecular":[29,42,62,80],"design":[30],"methods":[31],"are":[32],"limited":[33],"because":[34],"they":[35],"do":[36],"not":[37],"adequately":[38],"capture":[39],"the":[40,69,87,90,100,106,115,144],"ligand":[41,94,128],"position":[43],"information":[44],"Euclidean":[46],"We":[48,76],"proposed":[49],"diffusion":[51],"model":[52,104,124],"based":[53],"on":[54,99],"SE(3)-equivariant":[55],"graph":[56],"neural":[57],"networks":[58],"to":[59,65],"enhance":[60],"generated":[61],"binding":[63,145],"affinity":[64],"protein":[66,152],"targets":[67],"using":[68],"long-range":[70],"distance-aware":[72],"attention":[73],"head":[74],"mix.":[75],"also":[77],"presented":[78],"geometry":[81],"feature":[82],"enhancement":[83],"strategy,":[84],"further":[85],"strengthening":[86],"perception":[88],"of":[89,93,139],"spatial":[91],"size":[92],"molecules.":[95],"Results":[96],"show":[97],"that,":[98],"CrossDocked2020":[101],"dataset,":[102],"our":[103],"outperforms":[105],"existing":[107],"state-of-the-art":[108],"models":[109],"across":[110],"various":[111],"affinity-related":[112],"metrics,":[113],"including":[114],"Vina":[116],"Score,":[117],"preserves":[119],"essential":[120],"drug-like":[121],"properties.":[122],"Our":[123],"excels":[125],"designing":[127],"with":[130],"macrocyclic":[131],"structures.":[132],"Additionally,":[133],"it":[134],"offers":[135],"moderate":[137],"level":[138],"interpretability,":[140],"aiding":[141],"understanding":[143],"pockets.":[153]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-16T00:00:00"}
