{"id":"https://openalex.org/W7125822679","doi":"https://doi.org/10.1021/acs.jcim.5c02630","title":"Assessing Boltz-2 Performance for the Binding Classification of Docking Hits","display_name":"Assessing Boltz-2 Performance for the Binding Classification of Docking Hits","publication_year":2026,"publication_date":"2026-01-27","ids":{"openalex":"https://openalex.org/W7125822679","doi":"https://doi.org/10.1021/acs.jcim.5c02630","pmid":"https://pubmed.ncbi.nlm.nih.gov/41592323"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02630","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02630","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/A5123916258","display_name":"Guillaume Bret","orcid":null},"institutions":[{"id":"https://openalex.org/I4210116974","display_name":"Laboratoire d'Innovation Th\u00e9rapeutique","ror":"https://ror.org/02g4mxc89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210116974","https://openalex.org/I4210128300","https://openalex.org/I68947357"]},{"id":"https://openalex.org/I68947357","display_name":"Universit\u00e9 de Strasbourg","ror":"https://ror.org/00pg6eq24","country_code":"FR","type":"education","lineage":["https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Guillaume Bret","raw_affiliation_strings":["Laboratoire d\u2019innovation th\u00e9rapeutique","UMR7200 CNRS-Universit\u00e9 de Strasbourg"],"affiliations":[{"raw_affiliation_string":"Laboratoire d\u2019innovation th\u00e9rapeutique","institution_ids":["https://openalex.org/I4210116974"]},{"raw_affiliation_string":"UMR7200 CNRS-Universit\u00e9 de Strasbourg","institution_ids":["https://openalex.org/I68947357"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124018484","display_name":"Fran\u00e7ois Sindt","orcid":null},"institutions":[{"id":"https://openalex.org/I4210116974","display_name":"Laboratoire d'Innovation Th\u00e9rapeutique","ror":"https://ror.org/02g4mxc89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210116974","https://openalex.org/I4210128300","https://openalex.org/I68947357"]},{"id":"https://openalex.org/I68947357","display_name":"Universit\u00e9 de Strasbourg","ror":"https://ror.org/00pg6eq24","country_code":"FR","type":"education","lineage":["https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fran\u00e7ois Sindt","raw_affiliation_strings":["Laboratoire d\u2019innovation th\u00e9rapeutique","UMR7200 CNRS-Universit\u00e9 de Strasbourg"],"affiliations":[{"raw_affiliation_string":"Laboratoire d\u2019innovation th\u00e9rapeutique","institution_ids":["https://openalex.org/I4210116974"]},{"raw_affiliation_string":"UMR7200 CNRS-Universit\u00e9 de Strasbourg","institution_ids":["https://openalex.org/I68947357"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5123906881","display_name":"Didier Rognan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210116974","display_name":"Laboratoire d'Innovation Th\u00e9rapeutique","ror":"https://ror.org/02g4mxc89","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210116974","https://openalex.org/I4210128300","https://openalex.org/I68947357"]},{"id":"https://openalex.org/I68947357","display_name":"Universit\u00e9 de Strasbourg","ror":"https://ror.org/00pg6eq24","country_code":"FR","type":"education","lineage":["https://openalex.org/I68947357"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Didier Rognan","raw_affiliation_strings":["Laboratoire d\u2019innovation th\u00e9rapeutique","UMR7200 CNRS-Universit\u00e9 de Strasbourg"],"affiliations":[{"raw_affiliation_string":"Laboratoire d\u2019innovation th\u00e9rapeutique","institution_ids":["https://openalex.org/I4210116974"]},{"raw_affiliation_string":"UMR7200 CNRS-Universit\u00e9 de Strasbourg","institution_ids":["https://openalex.org/I68947357"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5123906881"],"corresponding_institution_ids":["https://openalex.org/I4210116974","https://openalex.org/I68947357"],"apc_list":null,"apc_paid":null,"fwci":22.2463,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.98151639,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"66","issue":"3","first_page":"1511","last_page":"1521"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6922000050544739,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.6922000050544739,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.18140000104904175,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.019700000062584877,"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/docking","display_name":"Docking (animal)","score":0.684499979019165},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.38989999890327454},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.37950000166893005},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.33309999108314514},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.32109999656677246},{"id":"https://openalex.org/keywords/binary-classification","display_name":"Binary classification","score":0.31929999589920044},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.30390000343322754},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.29789999127388}],"concepts":[{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.684499979019165},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5174000263214111},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5151000022888184},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48539999127388},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.40220001339912415},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.38989999890327454},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38749998807907104},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.37950000166893005},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3643999993801117},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.33309999108314514},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.32109999656677246},{"id":"https://openalex.org/C66905080","wikidata":"https://www.wikidata.org/wiki/Q17005494","display_name":"Binary classification","level":3,"score":0.31929999589920044},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.30390000343322754},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.29789999127388},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.2939999997615814},{"id":"https://openalex.org/C2780430158","wikidata":"https://www.wikidata.org/wiki/Q7685902","display_name":"Target protein","level":3,"score":0.28200000524520874},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.28029999136924744},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C24259465","wikidata":"https://www.wikidata.org/wiki/Q2272153","display_name":"Chemical similarity","level":3,"score":0.27149999141693115},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2685999870300293},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.26440000534057617},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2547999918460846},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.2513999938964844}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.5c02630","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02630","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:41592323","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41592323","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:HAL:hal-05486444v1","is_oa":false,"landing_page_url":"https://cnrs.hal.science/hal-05486444","pdf_url":null,"source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Chemical Information and Modeling, 2026, ⟨10.1021/acs.jcim.5c02630⟩","raw_type":"Journal articles"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7551889419555664,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1833104430","https://openalex.org/W1970613671","https://openalex.org/W2038009022","https://openalex.org/W2040990879","https://openalex.org/W2140673705","https://openalex.org/W2766694609","https://openalex.org/W2912171584","https://openalex.org/W2940516695","https://openalex.org/W3004731690","https://openalex.org/W3128627668","https://openalex.org/W3176155318","https://openalex.org/W3177828909","https://openalex.org/W4200208453","https://openalex.org/W4200233821","https://openalex.org/W4200289210","https://openalex.org/W4242360498","https://openalex.org/W4297995910","https://openalex.org/W4306728530","https://openalex.org/W4307468223","https://openalex.org/W4307722378","https://openalex.org/W4367672738","https://openalex.org/W4376131033","https://openalex.org/W4387639561","https://openalex.org/W4388455891","https://openalex.org/W4391780280","https://openalex.org/W4392544734","https://openalex.org/W4396721167","https://openalex.org/W4399070999","https://openalex.org/W4400251428","https://openalex.org/W4402625758","https://openalex.org/W4403324307","https://openalex.org/W4403966268","https://openalex.org/W4404458588","https://openalex.org/W4404511389","https://openalex.org/W4404565424","https://openalex.org/W4404642710","https://openalex.org/W4405468413","https://openalex.org/W4406274436","https://openalex.org/W4407276888","https://openalex.org/W4408195088","https://openalex.org/W4410599528","https://openalex.org/W4411463597","https://openalex.org/W4411965763","https://openalex.org/W4414850304"],"related_works":[],"abstract_inverted_index":{"The":[0],"recently":[1,23],"released":[2],"Boltz-2":[3,32,84,135],"cofolding":[4],"model":[5],"is":[6],"generating":[7],"high":[8],"expectations":[9],"by":[10,41,70],"enabling":[11],"both":[12],"protein-ligand":[13],"structure":[14],"and":[15,25,103,120],"binding":[16,79,117],"affinity":[17,56,95,136],"predictions.":[18,137],"When":[19],"applied":[20],"to":[21,59,74,115,125],"a":[22,42],"described":[24],"challenging":[26],"data":[27],"set":[28],"of":[29,63,90,108],"ultralarge-virtual-screening":[30],"hits,":[31],"excels":[33],"at":[34],"discriminating":[35],"true":[36],"from":[37],"false":[38],"positives,":[39],"overcoming":[40],"large":[43],"margin":[44],"all":[45],"scoring":[46],"functions":[47],"tested":[48],"so":[49],"far":[50],"on":[51,87,130],"raw":[52],"docking":[53],"poses.":[54],"Strikingly,":[55],"predictions":[57,96],"seem":[58],"be":[60],"relatively":[61],"independent":[62],"pose":[64],"quality":[65],"but":[66],"are":[67],"not":[68],"biased":[69],"obvious":[71],"chemical":[72],"similarity":[73],"known":[75],"compounds":[76,112],"sharing":[77],"comparable":[78],"potencies.":[80],"To":[81],"ascertain":[82],"that":[83],"truly":[85],"relies":[86],"the":[88,131],"physics":[89],"intermolecular":[91],"interactions,":[92],"we":[93],"challenged":[94],"with":[97],"biologically":[98],"meaningful":[99],"challenges":[100],"(target":[101],"mutation":[102],"target":[104,126],"shuffling).":[105],"Binary":[106],"classification":[107],"active":[109],"vs":[110],"inactive":[111],"remains":[113],"insensitive":[114],"key":[116],"site":[118],"mutations":[119],"even":[121],"in":[122],"some":[123],"cases":[124],"exchange,":[127],"raising":[128],"concerns":[129],"hidden":[132],"features":[133],"governing":[134]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2026-01-28T00:00:00"}