{"id":"https://openalex.org/W4410159318","doi":"https://doi.org/10.1186/s12859-025-06072-w","title":"Sculpting molecules in text-3D space: a flexible substructure aware framework for text-oriented molecular optimization","display_name":"Sculpting molecules in text-3D space: a flexible substructure aware framework for text-oriented molecular optimization","publication_year":2025,"publication_date":"2025-05-07","ids":{"openalex":"https://openalex.org/W4410159318","doi":"https://doi.org/10.1186/s12859-025-06072-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/40335938"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06072-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06072-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06072-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06072-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044546984","display_name":"Kaiwei Zhang","orcid":"https://orcid.org/0009-0006-8910-6283"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210156404","display_name":"Institute of Information Engineering","ror":"https://ror.org/04r53se39","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210156404"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kaiwei Zhang","raw_affiliation_strings":["Institute of Information Engineering, Chinese Academy of Sciences, Beijing, 100085, China"],"affiliations":[{"raw_affiliation_string":"Institute of Information Engineering, Chinese Academy of Sciences, Beijing, 100085, China","institution_ids":["https://openalex.org/I4210156404","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101314376","display_name":"Yange Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I2250955327","display_name":"Huawei Technologies (China)","ror":"https://ror.org/00cmhce21","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250955327"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yange Lin","raw_affiliation_strings":["Huawei Technologies, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"Huawei Technologies, Shenzhen, China","institution_ids":["https://openalex.org/I2250955327"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054389433","display_name":"Guangcheng Wu","orcid":"https://orcid.org/0000-0001-6112-9092"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"CN","type":"education","lineage":["https://openalex.org/I177725633"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Guangcheng Wu","raw_affiliation_strings":["Department of Chemistry, The University of Hong Kong, Hong Kong SAR, 999077, China"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, The University of Hong Kong, Hong Kong SAR, 999077, China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007581371","display_name":"Yuxiang Ren","orcid":"https://orcid.org/0000-0002-0760-796X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yuxiang Ren","raw_affiliation_strings":["Huawei Technologies, Shenzhen, China. renyuxiang1@huawei.com"],"affiliations":[{"raw_affiliation_string":"Huawei Technologies, Shenzhen, China. renyuxiang1@huawei.com","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091024831","display_name":"Xuecang Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I2250955327","display_name":"Huawei Technologies (China)","ror":"https://ror.org/00cmhce21","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250955327"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210156404","display_name":"Institute of Information Engineering","ror":"https://ror.org/04r53se39","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210156404"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuecang Zhang","raw_affiliation_strings":["Huawei Technologies, Shenzhen, China","Institute of Information Engineering, Chinese Academy of Sciences, Beijing, 100085, China"],"affiliations":[{"raw_affiliation_string":"Huawei Technologies, Shenzhen, China","institution_ids":["https://openalex.org/I2250955327"]},{"raw_affiliation_string":"Institute of Information Engineering, Chinese Academy of Sciences, Beijing, 100085, China","institution_ids":["https://openalex.org/I4210156404","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017233409","display_name":"Bo Wang","orcid":"https://orcid.org/0000-0001-7189-1531"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I2250955327","display_name":"Huawei Technologies (China)","ror":"https://ror.org/00cmhce21","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250955327"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Wang","raw_affiliation_strings":["Huawei Technologies, Shenzhen, China","School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China"],"affiliations":[{"raw_affiliation_string":"Huawei Technologies, Shenzhen, China","institution_ids":["https://openalex.org/I2250955327"]},{"raw_affiliation_string":"School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100419421","display_name":"Xiaoyu Zhang","orcid":"https://orcid.org/0000-0002-8125-754X"},"institutions":[{"id":"https://openalex.org/I2250955327","display_name":"Huawei Technologies (China)","ror":"https://ror.org/00cmhce21","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250955327"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210156404","display_name":"Institute of Information Engineering","ror":"https://ror.org/04r53se39","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210156404"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao-Yu Zhang","raw_affiliation_strings":["Huawei Technologies, Shenzhen, China","Institute of Information Engineering, Chinese Academy of Sciences, Beijing, 100085, China"],"affiliations":[{"raw_affiliation_string":"Huawei Technologies, Shenzhen, China","institution_ids":["https://openalex.org/I2250955327"]},{"raw_affiliation_string":"Institute of Information Engineering, Chinese Academy of Sciences, Beijing, 100085, China","institution_ids":["https://openalex.org/I4210156404","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100544782","display_name":"Weitao Du","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Weitao Du","raw_affiliation_strings":["Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China. duweitao@mail.ustc.edu.cn","Huawei Technologies, Shenzhen, China. duweitao@mail.ustc.edu.cn"],"affiliations":[{"raw_affiliation_string":"Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China. duweitao@mail.ustc.edu.cn","institution_ids":[]},{"raw_affiliation_string":"Huawei Technologies, Shenzhen, China. duweitao@mail.ustc.edu.cn","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5044546984"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210156404"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.3746,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.81967464,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"26","issue":"1","first_page":"123","last_page":"123"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9954000115394592,"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":0.9954000115394592,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9941999912261963,"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"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9746000170707703,"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/substructure","display_name":"Substructure","score":0.8693891763687134},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6393997073173523},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.5240645408630371},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4533417224884033},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.44428128004074097},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3279177248477936},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22523382306098938},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.14567264914512634},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13356900215148926},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07838720083236694}],"concepts":[{"id":"https://openalex.org/C99679407","wikidata":"https://www.wikidata.org/wiki/Q56761637","display_name":"Substructure","level":2,"score":0.8693891763687134},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6393997073173523},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.5240645408630371},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4533417224884033},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.44428128004074097},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3279177248477936},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22523382306098938},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.14567264914512634},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13356900215148926},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07838720083236694},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":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":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06072-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06072-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06072-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40335938","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40335938","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:efec052c91264d17bc9ea669f0c4b5f9","is_oa":true,"landing_page_url":"https://doaj.org/article/efec052c91264d17bc9ea669f0c4b5f9","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-26 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12060419","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12060419","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06072-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06072-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06072-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G37568934","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8504642471","display_name":null,"funder_award_id":"62376265","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410159318.pdf","grobid_xml":"https://content.openalex.org/works/W4410159318.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W1981323072","https://openalex.org/W2025006523","https://openalex.org/W2052856663","https://openalex.org/W2055358944","https://openalex.org/W2085760714","https://openalex.org/W2151697120","https://openalex.org/W2155653793","https://openalex.org/W2160592148","https://openalex.org/W2163279482","https://openalex.org/W2169678694","https://openalex.org/W2172216479","https://openalex.org/W2173027866","https://openalex.org/W2529996553","https://openalex.org/W2578240541","https://openalex.org/W2594183968","https://openalex.org/W2610148085","https://openalex.org/W2613900957","https://openalex.org/W2747592475","https://openalex.org/W2765224015","https://openalex.org/W2773987374","https://openalex.org/W2784226073","https://openalex.org/W2797867047","https://openalex.org/W2805483395","https://openalex.org/W2883583109","https://openalex.org/W2884414424","https://openalex.org/W2900090807","https://openalex.org/W2946612387","https://openalex.org/W2989615256","https://openalex.org/W2991736596","https://openalex.org/W3006759222","https://openalex.org/W3014154196","https://openalex.org/W3024385728","https://openalex.org/W3087318638","https://openalex.org/W3094640617","https://openalex.org/W3096418018","https://openalex.org/W3096433340","https://openalex.org/W3096831136","https://openalex.org/W3098269892","https://openalex.org/W3100358278","https://openalex.org/W3100751385","https://openalex.org/W3147983081","https://openalex.org/W3169299662","https://openalex.org/W3200806939","https://openalex.org/W3209056694","https://openalex.org/W3212070798","https://openalex.org/W3212417448","https://openalex.org/W4212837331","https://openalex.org/W4213077304","https://openalex.org/W4214868967","https://openalex.org/W4221161486","https://openalex.org/W4304203195","https://openalex.org/W4386804497","https://openalex.org/W4389071526","https://openalex.org/W4389888290","https://openalex.org/W4402727536","https://openalex.org/W6602311867","https://openalex.org/W6610450269","https://openalex.org/W6733974131","https://openalex.org/W6817647423"],"related_works":["https://openalex.org/W3153444835","https://openalex.org/W2153916713","https://openalex.org/W2023846184","https://openalex.org/W2703419385","https://openalex.org/W2329056228","https://openalex.org/W2284584236","https://openalex.org/W2950955148","https://openalex.org/W1979083399","https://openalex.org/W2344320748","https://openalex.org/W2374530195"],"abstract_inverted_index":{"The":[0],"integration":[1],"of":[2,26,32,112,200,227,238],"deep":[3,201],"learning,":[4],"particularly":[5],"AI-Generated":[6],"Content,":[7],"with":[8,69,241],"high-quality":[9],"data":[10],"derived":[11],"from":[12],"ab":[13],"initio":[14],"calculations":[15],"has":[16],"emerged":[17],"as":[18,93],"a":[19,44,51,94,103,161,210,221],"promising":[20],"avenue":[21],"for":[22,109,187,197,209,220],"transforming":[23],"the":[24,30,59,110,150,173,185,198,207,228,236],"landscape":[25],"scientific":[27],"research.":[28],"However,":[29],"challenge":[31],"designing":[33],"molecular":[34,53,113,137,214,239],"drugs":[35],"or":[36],"materials":[37],"that":[38],"incorporate":[39],"multi-modality":[40,95],"prior":[41,188],"knowledge":[42],"remains":[43],"critical":[45],"and":[46,66,128,144,224,244],"complex":[47],"undertaking.":[48],"Specifically,":[49],"achieving":[50],"practical":[52],"design":[54,88,215],"necessitates":[55],"not":[56,192],"only":[57,193],"meeting":[58],"diversity":[60],"requirements":[61],"but":[62,204],"also":[63,205],"addressing":[64],"structural":[65,130,143],"textural":[67,145],"constraints":[68,146],"various":[70],"symmetries":[71],"outlined":[72],"by":[73,90,147],"domain":[74],"experts.":[75],"In":[76],"this":[77,86],"article,":[78],"we":[79],"present":[80],"an":[81],"innovative":[82],"approach":[83],"to":[84,120,135,140,167,175],"tackle":[85],"inverse":[87],"problem":[89],"formulating":[91],"it":[92],"guidance":[96,156],"optimization":[97,114,157,164],"task.":[98],"Our":[99],"proposed":[100],"solution":[101],"involves":[102],"textural-structure":[104],"alignment":[105],"symmetric":[106,142],"diffusion":[107],"framework":[108],"implementation":[111],"tasks,":[115],"namely":[116],"3DToMolo.":[117],"3DToMolo":[118,171,217],"aims":[119],"harmonize":[121],"diverse":[122],"modalities":[123],"including":[124],"textual":[125],"description":[126],"features":[127],"graph":[129],"features,":[131],"aligning":[132],"them":[133],"seamlessly":[134],"produce":[136],"structures":[138],"adhere":[139],"specified":[141,181],"experts":[148],"in":[149,213,235],"field.":[151],"Experimental":[152],"trials":[153],"across":[154],"three":[155],"settings":[158],"have":[159],"shown":[160],"superior":[162],"hit":[163],"performance":[165],"compared":[166],"state-of-the-art":[168],"methodologies.":[169],"Moreover,":[170],"demonstrates":[172],"capability":[174],"discover":[176],"potential":[177],"novel":[178],"molecules,":[179],"incorporating":[180],"target":[182],"substructures,":[183],"without":[184],"need":[186],"knowledge.":[189],"This":[190],"work":[191],"holds":[194],"general":[195],"significance":[196],"advancement":[199],"learning":[202],"methodologies":[203],"paves":[206],"way":[208],"transformative":[211],"shift":[212],"strategies.":[216],"creates":[218],"opportunities":[219],"more":[222],"nuanced":[223],"effective":[225],"exploration":[226],"vast":[229],"chemical":[230],"space,":[231],"opening":[232],"new":[233],"frontiers":[234],"development":[237],"entities":[240],"tailored":[242],"properties":[243],"functionalities.":[245]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
