{"id":"https://openalex.org/W7154135997","doi":"https://doi.org/10.1021/acs.jcim.6c00044","title":"De Novo Molecular Design via Shape-Constrained Diffusion Models","display_name":"De Novo Molecular Design via Shape-Constrained Diffusion Models","publication_year":2026,"publication_date":"2026-04-13","ids":{"openalex":"https://openalex.org/W7154135997","doi":"https://doi.org/10.1021/acs.jcim.6c00044","pmid":"https://pubmed.ncbi.nlm.nih.gov/41973903"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6c00044","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c00044","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5133550341","display_name":"Bohao Li","orcid":"https://orcid.org/0009-0004-0627-806X"},"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":"Bohao Li","raw_affiliation_strings":["Guangzhou National Laboratory","School of Computer Science and Engineering","Sun Yat-Sen University"],"raw_orcid":"https://orcid.org/0009-0004-0627-806X","affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]},{"raw_affiliation_string":"School of Computer Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Sun Yat-Sen University","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128065845","display_name":"Xinyu Wu","orcid":null},"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":"Xinyu Wu","raw_affiliation_strings":["Guangzhou National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055090280","display_name":"Yu Cao","orcid":"https://orcid.org/0000-0001-5767-7029"},"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":"Yu Cao","raw_affiliation_strings":["Guangzhou National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jie Lin","orcid":null},"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":"Jie Lin","raw_affiliation_strings":["Guangzhou National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003734080","display_name":"Jingpeng Zhong","orcid":null},"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":"Jingpeng Zhong","raw_affiliation_strings":["Guangzhou National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055386790","display_name":"Hua Chen","orcid":"https://orcid.org/0000-0002-2320-3228"},"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"]},{"id":"https://openalex.org/I92039509","display_name":"Guangzhou Medical University","ror":"https://ror.org/00zat6v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I92039509"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hua Chen","raw_affiliation_strings":["Guangzhou Medical University","Guangzhou National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou Medical University","institution_ids":["https://openalex.org/I92039509"]},{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hua Chen","orcid":null},"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"]},{"id":"https://openalex.org/I92039509","display_name":"Guangzhou Medical University","ror":"https://ror.org/00zat6v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I92039509"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hua Chen","raw_affiliation_strings":["Guangzhou Medical University","Guangzhou National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou Medical University","institution_ids":["https://openalex.org/I92039509"]},{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yongzhi Lu","orcid":null},"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":"Yongzhi Lu","raw_affiliation_strings":["Guangzhou National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Miru Tang","orcid":null},"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":"Miru Tang","raw_affiliation_strings":["Guangzhou National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":null,"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"],"raw_orcid":"https://orcid.org/0000-0002-6888-2973","affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Science","institution_ids":[]},{"raw_affiliation_string":"Sun Yat-sen University","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Ting Ran","orcid":null},"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":"Ting Ran","raw_affiliation_strings":["Guangzhou National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016431337","display_name":"Mengning Xu","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Yuedong Yang","raw_affiliation_strings":["School of Computer Science and Engineering","Sun Yat-Sen University"],"raw_orcid":"https://orcid.org/0000-0002-6782-2813","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Sun Yat-Sen University","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133528045","display_name":"Jinsai Shang","orcid":"https://orcid.org/0009-0004-4557-2974"},"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":true,"raw_author_name":"Mingyuan Xu","raw_affiliation_strings":["Guangzhou National Laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jinsai Shang","orcid":"https://orcid.org/0009-0004-4557-2974"},"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"]},{"id":"https://openalex.org/I92039509","display_name":"Guangzhou Medical University","ror":"https://ror.org/00zat6v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I92039509"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jinsai Shang","raw_affiliation_strings":["Guangzhou Medical University","Guangzhou National Laboratory"],"raw_orcid":"https://orcid.org/0009-0004-4557-2974","affiliations":[{"raw_affiliation_string":"Guangzhou Medical University","institution_ids":["https://openalex.org/I92039509"]},{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"middle","author":{"id":null,"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"]},{"id":"https://openalex.org/I92039509","display_name":"Guangzhou Medical University","ror":"https://ror.org/00zat6v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I92039509"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hongming Chen","raw_affiliation_strings":["Guangzhou Medical University","Guangzhou National Laboratory"],"raw_orcid":"https://orcid.org/0000-0002-8065-8333","affiliations":[{"raw_affiliation_string":"Guangzhou Medical University","institution_ids":["https://openalex.org/I92039509"]},{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]},{"author_position":"last","author":{"id":null,"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"]},{"id":"https://openalex.org/I92039509","display_name":"Guangzhou Medical University","ror":"https://ror.org/00zat6v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I92039509"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongming Chen","raw_affiliation_strings":["Guangzhou Medical University","Guangzhou National Laboratory"],"raw_orcid":"https://orcid.org/0000-0002-8065-8333","affiliations":[{"raw_affiliation_string":"Guangzhou Medical University","institution_ids":["https://openalex.org/I92039509"]},{"raw_affiliation_string":"Guangzhou National Laboratory","institution_ids":["https://openalex.org/I4210090512"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5016431337","https://openalex.org/A5133528045"],"corresponding_institution_ids":["https://openalex.org/I4210090512","https://openalex.org/I92039509"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.39406668,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"8","first_page":"4592","last_page":"4606"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.06279999762773514,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.06279999762773514,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11798","display_name":"Optimal Experimental Design Methods","score":0.05730000138282776,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.040699999779462814,"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/diffusion","display_name":"Diffusion","score":0.5087000131607056},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.24040000140666962},{"id":"https://openalex.org/keywords/agr\u00e9gation","display_name":"Agr\u00e9gation","score":0.2168000042438507}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5156000256538391},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.5087000131607056},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.30799999833106995},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.26809999346733093},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2667999863624573},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.24040000140666962},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23549999296665192},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.23190000653266907},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.22130000591278076},{"id":"https://openalex.org/C2778207910","wikidata":"https://www.wikidata.org/wiki/Q397610","display_name":"Agr\u00e9gation","level":3,"score":0.2168000042438507}],"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":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D066246","descriptor_name":"ErbB Receptors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.6c00044","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c00044","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:41973903","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41973903","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1985588649","https://openalex.org/W1988037271","https://openalex.org/W2027065525","https://openalex.org/W2075186867","https://openalex.org/W2144659448","https://openalex.org/W2172140247","https://openalex.org/W2176516200","https://openalex.org/W2578240541","https://openalex.org/W2789074794","https://openalex.org/W2902812092","https://openalex.org/W2914635984","https://openalex.org/W2963028280","https://openalex.org/W3034806393","https://openalex.org/W3116865743","https://openalex.org/W3162554793","https://openalex.org/W3209790821","https://openalex.org/W3213530673","https://openalex.org/W4297951436","https://openalex.org/W4320342349","https://openalex.org/W4320857994","https://openalex.org/W4382239902","https://openalex.org/W4386804497","https://openalex.org/W4386845335","https://openalex.org/W4389257854","https://openalex.org/W4389696354","https://openalex.org/W4390873054","https://openalex.org/W4394718179","https://openalex.org/W4404995526","https://openalex.org/W4405194591"],"related_works":[],"abstract_inverted_index":{"Generative":[0],"models":[1],"that":[2,26,38,114],"preserve":[3],"3D":[4,31,41,73],"shape":[5,74],"similarity":[6],"while":[7,79],"enabling":[8],"structural":[9],"novelty":[10,90],"remain":[11],"a":[12,23,28,34,40,136],"central":[13],"challenge":[14],"in":[15],"de":[16],"novo":[17],"molecular":[18,143],"design.":[19],"We":[20],"present":[21],"Diff-Shape,":[22],"diffusion-based":[24],"framework":[25],"couples":[27],"pretrained":[29],"unconditional":[30],"generator":[32],"with":[33],"Graph":[35],"ControlNet":[36],"constraint":[37],"ingests":[39],"reference":[42],"shape.":[43],"By":[44],"integrating":[45],"substructure":[46],"inpainting,":[47],"Diff-Shape":[48,67,134],"enables":[49],"controllable,":[50],"shape-guided":[51],"design":[52],"across":[53,89],"tasks":[54],"such":[55],"as":[56,135],"scaffold":[57,59],"hopping,":[58],"decoration,":[60],"and":[61,94,107,120,138],"linker":[62],"generation.":[63,144],"On":[64],"comprehensive":[65],"benchmarks,":[66],"achieves":[68],"substantially":[69],"higher":[70],"rates":[71],"of":[72],"fidelity":[75],"than":[76],"state-of-the-art":[77],"methods,":[78],"maintaining":[80],"low":[81],"2D":[82],"graph":[83],"similarity.":[84],"These":[85],"improvements":[86],"are":[87],"robust":[88],"thresholds,":[91],"noise":[92],"levels,":[93],"diverse":[95],"references.":[96],"Finally,":[97],"case":[98],"studies":[99],"on":[100],"Kirsten":[101],"rat":[102],"sarcoma":[103],"virus":[104],"(KRAS)":[105],"G12D":[106],"epidermal":[108],"growth":[109],"factor":[110],"receptor":[111],"L858R/T790M/C797S":[112],"demonstrate":[113],"several":[115],"designed":[116],"candidates":[117],"were":[118],"synthesized":[119],"exhibit":[121],"nanomolar":[122],"biochemical":[123],"potency,":[124],"underscoring":[125],"the":[126],"method's":[127],"translational":[128],"relevance.":[129],"Together,":[130],"these":[131],"results":[132],"position":[133],"powerful":[137],"generalizable":[139],"approach":[140],"for":[141],"shape-constrained":[142]},"counts_by_year":[],"updated_date":"2026-07-20T07:56:41.581041","created_date":"2026-04-14T00:00:00"}