{"id":"https://openalex.org/W4405905364","doi":"https://doi.org/10.1093/bib/bbae676","title":"GADIFF: a transferable graph attention diffusion model for generating molecular conformations","display_name":"GADIFF: a transferable graph attention diffusion model for generating molecular conformations","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4405905364","doi":"https://doi.org/10.1093/bib/bbae676","pmid":"https://pubmed.ncbi.nlm.nih.gov/39737569"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae676","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae676","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae676/61294692/bbae676.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/26/1/bbae676/61294692/bbae676.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058597447","display_name":"Donghan Wang","orcid":"https://orcid.org/0000-0002-4912-6355"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Donghan Wang","raw_affiliation_strings":["School of Information Science and Technology, Northeast Normal University , 130117 Changchun ,"],"raw_orcid":"https://orcid.org/0000-0002-4912-6355","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University , 130117 Changchun ,","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111028160","display_name":"Xu Dong","orcid":"https://orcid.org/0009-0003-9778-3290"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xu Dong","raw_affiliation_strings":["School of Information Science and Technology, Northeast Normal University , 130117 Changchun ,"],"raw_orcid":"https://orcid.org/0009-0003-9778-3290","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University , 130117 Changchun ,","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014810470","display_name":"Xueyou Zhang","orcid":"https://orcid.org/0009-0002-4161-2225"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xueyou Zhang","raw_affiliation_strings":["School of Information Science and Technology, Northeast Normal University , 130117 Changchun ,"],"raw_orcid":"https://orcid.org/0009-0002-4161-2225","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University , 130117 Changchun ,","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044442113","display_name":"Lihong Hu","orcid":"https://orcid.org/0000-0003-3792-2917"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"LiHong Hu","raw_affiliation_strings":["School of Information Science and Technology, Northeast Normal University , 130117 Changchun ,"],"raw_orcid":"https://orcid.org/0000-0003-3792-2917","affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University , 130117 Changchun ,","institution_ids":["https://openalex.org/I184983240"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I184983240"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.5586,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.85194815,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"26","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9912999868392944,"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/T12748","display_name":"Molecular spectroscopy and chirality","score":0.9787999987602234,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5670604705810547},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4781978130340576},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.4373423457145691},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.20627331733703613},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09553560614585876},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.06882268190383911}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5670604705810547},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4781978130340576},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.4373423457145691},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.20627331733703613},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09553560614585876},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.06882268190383911}],"mesh":[{"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":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":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":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae676","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae676","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae676/61294692/bbae676.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:39737569","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39737569","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:11684900","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11684900","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11684900/pdf/bbae676.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae676","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae676","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae676/61294692/bbae676.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/G1490283651","display_name":null,"funder_award_id":"22273010","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7070060253","display_name":null,"funder_award_id":"20210402075GH","funder_id":"https://openalex.org/F4320327282","funder_display_name":"Department of Science and Technology of Jilin Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322174","display_name":"People's Government of Jilin Province","ror":"https://ror.org/02fzqav45"},{"id":"https://openalex.org/F4320327282","display_name":"Department of Science and Technology of Jilin Province","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405905364.pdf","grobid_xml":"https://content.openalex.org/works/W4405905364.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W569478347","https://openalex.org/W2007490029","https://openalex.org/W2018120102","https://openalex.org/W2024829861","https://openalex.org/W2063267830","https://openalex.org/W2127463492","https://openalex.org/W2136567909","https://openalex.org/W2244785476","https://openalex.org/W2266733933","https://openalex.org/W2271736303","https://openalex.org/W2314431251","https://openalex.org/W2332924377","https://openalex.org/W2560674852","https://openalex.org/W2726184500","https://openalex.org/W2931367569","https://openalex.org/W2953018250","https://openalex.org/W3006781192","https://openalex.org/W3009761974","https://openalex.org/W3024385728","https://openalex.org/W3034806393","https://openalex.org/W3087680971","https://openalex.org/W3105259638","https://openalex.org/W4200454557","https://openalex.org/W4226060238","https://openalex.org/W4226211505","https://openalex.org/W4310895557","https://openalex.org/W4317384333","https://openalex.org/W4323065907","https://openalex.org/W4389326437","https://openalex.org/W6768104975","https://openalex.org/W6779823529","https://openalex.org/W6788624270","https://openalex.org/W6795208335","https://openalex.org/W6795535946","https://openalex.org/W6797035790","https://openalex.org/W6803460408","https://openalex.org/W6810026998","https://openalex.org/W6810483326","https://openalex.org/W6850031907","https://openalex.org/W6852575741"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"The":[0,199,233],"diffusion":[1,21],"generative":[2],"model":[3,149,158,222],"has":[4],"achieved":[5],"remarkable":[6],"performance":[7,107],"across":[8],"various":[9],"research":[10],"fields.":[11],"In":[12,85,131],"this":[13],"study,":[14],"we":[15,87],"propose":[16],"a":[17,25,151,156,182,187],"transferable":[18,221],"graph":[19,188],"attention":[20,72],"model,":[22,184],"GADIFF,":[23],"for":[24,126,169,190,227],"molecular":[26,77,97,173,192,197,202],"conformation":[27,98,212],"generation":[28,117],"task.":[29],"With":[30],"adopting":[31],"multiple":[32],"equivariant":[33],"networks":[34],"in":[35,114],"the":[36,81,102,134,137,146,195,209,219,228],"Markov":[37],"chain,":[38],"GADIFF":[39,104,163,177,238],"adds":[40],"GIN":[41],"(Graph":[42],"Isomorphism":[43],"Network)":[44],"to":[45,74,90,95,166],"acquire":[46],"local":[47],"information":[48],"of":[49,83,116,211,230,237],"subgraphs":[50],"with":[51,109,145,178],"different":[52],"edge":[53],"types":[54],"(atomic":[55],"bonds,":[56],"bond":[57],"angle":[58,61],"interactions,":[59,62],"torsion":[60],"long-range":[63],"interactions)":[64],"and":[65,123,128,185,213,235],"applies":[66],"MSA":[67,89],"(Multi-head":[68],"Self-attention)":[69],"as":[70,181,206],"noise":[71,93,99],"mechanism":[73],"capture":[75],"global":[76],"information,":[78],"which":[79],"improves":[80],"representative":[82],"features.":[84],"addition,":[86],"utilize":[88],"calculate":[91],"dynamic":[92],"weights":[94],"boost":[96],"prediction.":[100],"Upon":[101],"improvements,":[103],"achieves":[105],"competitive":[106],"compared":[108,144],"recently":[110],"reported":[111],"state-of-the-art":[112],"models":[113],"terms":[115],"diversity(COV-R,":[118],"COV-P),":[119],"accuracy":[120],"(MAT-R,":[121],"MAT-P),":[122],"property":[124,214],"prediction":[125],"GEOM-QM9":[127,179],"GEOM-Drugs":[129,135],"datasets.":[130],"particular,":[132],"on":[133,162],"dataset,":[136],"average":[138],"COV-R":[139],"is":[140,164,239],"improved":[141],"by":[142,208],"3.75%":[143],"best":[147],"baseline":[148],"at":[150,194],"threshold":[152],"(1.25":[153],"\u00c5).":[154],"Furthermore,":[155],"transfer":[157],"named":[159],"GADIFF-NCI":[160],"based":[161],"developed":[165],"generate":[167],"conformations":[168,203],"noncovalent":[170],"interaction":[171],"(NCI)":[172],"systems.":[174],"It":[175],"takes":[176],"dataset":[180],"pre-trained":[183],"incorporates":[186],"encoder":[189],"learning":[191],"vectors":[193],"NCI":[196,201],"level.":[198],"resulting":[200],"are":[204],"reasonable,":[205],"assessed":[207],"evaluation":[210],"predictions.":[215],"This":[216],"suggests":[217],"that":[218],"proposed":[220],"may":[223],"hold":[224],"noteworthy":[225],"value":[226],"study":[229],"multi-molecular":[231],"conformations.":[232],"code":[234],"data":[236],"freely":[240],"downloaded":[241],"from":[242],"https://github.com/WangDHg/GADIFF.":[243]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4}],"updated_date":"2026-07-16T13:24:37.021932","created_date":"2025-10-10T00:00:00"}
