{"id":"https://openalex.org/W4407366140","doi":"https://doi.org/10.1021/acs.jcim.4c01896","title":"AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction","display_name":"AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction","publication_year":2025,"publication_date":"2025-02-11","ids":{"openalex":"https://openalex.org/W4407366140","doi":"https://doi.org/10.1021/acs.jcim.4c01896","pmid":"https://pubmed.ncbi.nlm.nih.gov/39933880"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01896","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01896","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.4c01896","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058064658","display_name":"Andr\u00e9 Brasil Vieira Wyzykowski","orcid":"https://orcid.org/0000-0002-2279-4177"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 Brasil Vieira Wyzykowski","raw_affiliation_strings":["Department of Biochemistry & Molecular Biology Michigan State University","Department of Biochemistry & Molecular Biology Michigan State University, East Lansing, Michigan 48824, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology Michigan State University","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology Michigan State University, East Lansing, Michigan 48824, United States","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024263070","display_name":"Fatemeh Fathi Niazi","orcid":null},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fatemeh Fathi Niazi","raw_affiliation_strings":["Department of Computational Mathematics","Science & Engineering Michigan State University","Department of Computational Mathematics, Science & Engineering Michigan State University, East Lansing, Michigan 48824, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational Mathematics","institution_ids":[]},{"raw_affiliation_string":"Science & Engineering Michigan State University","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Computational Mathematics, Science & Engineering Michigan State University, East Lansing, Michigan 48824, United States","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054841813","display_name":"Alex Dickson","orcid":"https://orcid.org/0000-0002-9640-1380"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alex Dickson","raw_affiliation_strings":["Department of Biochemistry & Molecular Biology Michigan State University","Department of Computational Mathematics","Science & Engineering Michigan State University","Department of Computational Mathematics, Science & Engineering Michigan State University, East Lansing, Michigan 48824, United States","Department of Biochemistry & Molecular Biology Michigan State University, East Lansing, Michigan 48824, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology Michigan State University","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Computational Mathematics","institution_ids":[]},{"raw_affiliation_string":"Science & Engineering Michigan State University","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Computational Mathematics, Science & Engineering Michigan State University, East Lansing, Michigan 48824, United States","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Biochemistry & Molecular Biology Michigan State University, East Lansing, Michigan 48824, United States","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5054841813"],"corresponding_institution_ids":["https://openalex.org/I87216513"],"apc_list":null,"apc_paid":null,"fwci":5.6172,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.95275048,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"65","issue":"4","first_page":"1798","last_page":"1811"},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9988999962806702,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9886000156402588,"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":0.5668890476226807},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.5155115127563477},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3216649293899536},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2296706736087799},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19249770045280457},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.13599807024002075}],"concepts":[{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.5668890476226807},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.5155115127563477},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3216649293899536},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2296706736087799},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19249770045280457},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.13599807024002075}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine 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":"D000465","descriptor_name":"Algorithms","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":"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":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","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":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","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":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.4c01896","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01896","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39933880","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39933880","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},{"id":"pmh:oai:pubmedcentral.nih.gov:11863375","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11863375","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11863375/pdf/ci4c01896.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c01896","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01896","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4699999988079071,"display_name":"Climate action","id":"https://metadata.un.org/sdg/13"}],"awards":[{"id":"https://openalex.org/G1685817841","display_name":null,"funder_award_id":"R01GM130794","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2652197547","display_name":null,"funder_award_id":"R01GM130794","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3611247453","display_name":null,"funder_award_id":"R01GM","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1583837637","https://openalex.org/W1971698657","https://openalex.org/W1999297737","https://openalex.org/W2001860413","https://openalex.org/W2012495996","https://openalex.org/W2034484539","https://openalex.org/W2035828432","https://openalex.org/W2040809566","https://openalex.org/W2040907622","https://openalex.org/W2087915438","https://openalex.org/W2130390906","https://openalex.org/W2149655632","https://openalex.org/W2163646378","https://openalex.org/W2516321997","https://openalex.org/W2612690371","https://openalex.org/W2898183010","https://openalex.org/W2912212024","https://openalex.org/W2931367569","https://openalex.org/W2968734407","https://openalex.org/W3014339631","https://openalex.org/W3034806393","https://openalex.org/W3105259638","https://openalex.org/W3109302196","https://openalex.org/W3110901318","https://openalex.org/W3121586850","https://openalex.org/W3175735871","https://openalex.org/W3198168376","https://openalex.org/W4225405705","https://openalex.org/W4313062391","https://openalex.org/W4327555752","https://openalex.org/W4360884927","https://openalex.org/W4385190718","https://openalex.org/W4387195417","https://openalex.org/W4389786948","https://openalex.org/W4405905364"],"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":{"Accurate":[0],"prediction":[1,16,181],"of":[2,123,131,137,157,163,182],"molecular":[3,35,75,173,183],"geometries":[4],"is":[5],"crucial":[6],"for":[7,50,71],"drug":[8,190],"discovery":[9],"and":[10,37,73,90,102,113,133,159,179,192],"materials":[11,193],"science.":[12],"Existing":[13],"fast":[14],"conformer":[15],"algorithms":[17],"often":[18],"rely":[19],"on":[20,109],"approximate":[21],"empirical":[22],"energy":[23,54],"functions,":[24],"resulting":[25],"in":[26],"low":[27],"accuracy.":[28],"More":[29],"accurate":[30,74,180],"methods":[31],"like":[32],"ab":[33],"initio":[34],"dynamics":[36],"Markov":[38],"chain":[39],"Monte":[40],"Carlo":[41],"can":[42],"be":[43],"computationally":[44],"expensive":[45],"due":[46],"to":[47,171,187],"the":[48,87,111,141],"need":[49],"evaluating":[51],"quantum":[52],"mechanical":[53],"functions.":[55],"To":[56],"address":[57],"this,":[58],"we":[59],"introduce":[60],"AGDIFF,":[61],"a":[62,120,128,134,154,160],"novel":[63],"machine":[64],"learning":[65],"framework":[66],"that":[67],"utilizes":[68],"diffusion":[69],"models":[70,81],"efficient":[72,178],"structure":[76],"prediction.":[77],"AGDIFF":[78,106,126,152],"extends":[79],"previous":[80],"(such":[82],"as":[83],"GeoDiff)":[84],"by":[85],"enhancing":[86],"global,":[88],"local,":[89],"edge":[91],"encoders":[92],"with":[93,119],"attention":[94],"mechanisms,":[95],"an":[96],"improved":[97],"SchNet":[98],"architecture,":[99],"batch":[100],"normalization,":[101],"feature":[103],"expansion":[104],"techniques.":[105],"outperforms":[107],"GeoDiff":[108],"both":[110],"GEOM-QM9":[112],"GEOM-Drugs":[114,144],"data":[115,145],"sets.":[116],"For":[117],"GEOM-QM9,":[118],"threshold":[121],"(\u03b4)":[122],"0.5":[124],"\u00c5,":[125,151],"achieves":[127],"mean":[129,135,161],"COV-R":[130,156],"93.08%":[132],"MAT-R":[136,162],"0.1965":[138],"\u00c5.":[139,165],"On":[140],"more":[142,177],"complex":[143],"set,":[146],"using":[147],"\u03b4":[148],"=":[149],"1.25":[150],"attains":[153],"median":[155],"100.00%":[158],"0.8237":[164],"These":[166],"findings":[167],"demonstrate":[168],"AGDIFF's":[169],"potential":[170],"advance":[172],"modeling":[174],"techniques,":[175],"enabling":[176],"geometries,":[184],"thus":[185],"contributing":[186],"computational":[188],"chemistry,":[189],"discovery,":[191],"design.":[194],"https://github.com/ADicksonLab/AGDIFF.":[195]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-02-12T00:00:00"}
