{"id":"https://openalex.org/W4411463597","doi":"https://doi.org/10.1101/2025.06.14.659707","title":"Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction","display_name":"Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction","publication_year":2025,"publication_date":"2025-06-18","ids":{"openalex":"https://openalex.org/W4411463597","doi":"https://doi.org/10.1101/2025.06.14.659707","pmid":"https://pubmed.ncbi.nlm.nih.gov/40667369"},"language":"en","primary_location":{"id":"doi:10.1101/2025.06.14.659707","doi":"https://doi.org/10.1101/2025.06.14.659707","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.06.14.659707","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.1101/2025.06.14.659707","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068703084","display_name":"Saro Passaro","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Saro Passaro","raw_affiliation_strings":["MIT CSAIL","MIT Jameel Clinic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MIT CSAIL","institution_ids":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"raw_affiliation_string":"MIT Jameel Clinic","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057871229","display_name":"Gabriele Corso","orcid":"https://orcid.org/0000-0002-1963-8755","observed_orcids":["https://orcid.org/0000-0002-1963-8755"]},"institutions":[{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gabriele Corso","raw_affiliation_strings":["MIT CSAIL","MIT Jameel Clinic"],"raw_orcid":"https://orcid.org/0000-0002-1963-8755","affiliations":[{"raw_affiliation_string":"MIT CSAIL","institution_ids":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"raw_affiliation_string":"MIT Jameel Clinic","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082461467","display_name":"Jeremy Wohlwend","orcid":"https://orcid.org/0000-0002-1993-2380","observed_orcids":["https://orcid.org/0000-0002-1993-2380"]},"institutions":[{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy Wohlwend","raw_affiliation_strings":["MIT CSAIL","MIT Jameel Clinic"],"raw_orcid":"https://orcid.org/0000-0002-1993-2380","affiliations":[{"raw_affiliation_string":"MIT CSAIL","institution_ids":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"raw_affiliation_string":"MIT Jameel Clinic","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060867169","display_name":"Mateo Reveiz","orcid":"https://orcid.org/0000-0002-5680-4150","observed_orcids":["https://orcid.org/0000-0002-5680-4150"]},"institutions":[{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mateo Reveiz","raw_affiliation_strings":["MIT CSAIL","MIT Jameel Clinic"],"raw_orcid":"https://orcid.org/0000-0002-5680-4150","affiliations":[{"raw_affiliation_string":"MIT CSAIL","institution_ids":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"raw_affiliation_string":"MIT Jameel Clinic","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071571459","display_name":"Stephan Thaler","orcid":"https://orcid.org/0000-0001-5383-1615","observed_orcids":["https://orcid.org/0000-0001-5383-1615"]},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephan Thaler","raw_affiliation_strings":["Recursion","Valence Labs"],"raw_orcid":"https://orcid.org/0000-0001-5383-1615","affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]},{"raw_affiliation_string":"Valence Labs","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012337744","display_name":"Vignesh Ram Somnath","orcid":"https://orcid.org/0000-0003-3894-646X","observed_orcids":["https://orcid.org/0000-0003-3894-646X"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Vignesh Ram Somnath","raw_affiliation_strings":["ETH Zurich"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ETH Zurich","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5118396049","display_name":"Noah Getz","orcid":"https://orcid.org/0009-0008-3676-3401","observed_orcids":["https://orcid.org/0009-0008-3676-3401"]},"institutions":[{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Noah Getz","raw_affiliation_strings":["MIT CSAIL","MIT Jameel Clinic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MIT CSAIL","institution_ids":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"raw_affiliation_string":"MIT Jameel Clinic","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135426700","display_name":"Tally Portnoi","orcid":"https://orcid.org/0000-0002-8543-7855","observed_orcids":["https://orcid.org/0000-0002-8543-7855"]},"institutions":[{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tally Portnoi","raw_affiliation_strings":["MIT CSAIL","MIT Jameel Clinic"],"raw_orcid":"https://orcid.org/0000-0002-8543-7855","affiliations":[{"raw_affiliation_string":"MIT CSAIL","institution_ids":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"raw_affiliation_string":"MIT Jameel Clinic","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5118396050","display_name":"Julien Roy","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julien Roy","raw_affiliation_strings":["Recursion","Valence Labs"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]},{"raw_affiliation_string":"Valence Labs","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Hannes Stark","orcid":"https://orcid.org/0000-0002-4463-326X","observed_orcids":["https://orcid.org/0000-0002-4463-326X"]},"institutions":[{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hannes Stark","raw_affiliation_strings":["MIT CSAIL","MIT Jameel Clinic"],"raw_orcid":"https://orcid.org/0000-0002-4463-326X","affiliations":[{"raw_affiliation_string":"MIT CSAIL","institution_ids":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"raw_affiliation_string":"MIT Jameel Clinic","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5118396048","display_name":"David Kwabi-Addo","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Kwabi-Addo","raw_affiliation_strings":["MIT CSAIL","MIT Jameel Clinic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MIT CSAIL","institution_ids":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"raw_affiliation_string":"MIT Jameel Clinic","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064214996","display_name":"Dominique Beaini","orcid":"https://orcid.org/0000-0002-4613-9388","observed_orcids":["https://orcid.org/0000-0002-4613-9388"]},"institutions":[{"id":"https://openalex.org/I4210159509","display_name":"Recursion (United States)","ror":"https://ror.org/05czpzc54","country_code":"US","type":"company","lineage":["https://openalex.org/I4210159509"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dominique Beaini","raw_affiliation_strings":["Recursion","Valence Labs"],"raw_orcid":"https://orcid.org/0000-0002-4613-9388","affiliations":[{"raw_affiliation_string":"Recursion","institution_ids":["https://openalex.org/I4210159509"]},{"raw_affiliation_string":"Valence Labs","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048915657","display_name":"Tommi Jaakkola","orcid":"https://orcid.org/0000-0002-2199-0379","observed_orcids":["https://orcid.org/0000-0002-2199-0379"]},"institutions":[{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tommi Jaakkola","raw_affiliation_strings":["MIT CSAIL","MIT Jameel Clinic"],"raw_orcid":"https://orcid.org/0000-0002-2199-0379","affiliations":[{"raw_affiliation_string":"MIT CSAIL","institution_ids":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"raw_affiliation_string":"MIT Jameel Clinic","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010124873","display_name":"Regina Barzilay","orcid":"https://orcid.org/0000-0002-2921-8201","observed_orcids":["https://orcid.org/0000-0002-2921-8201"]},"institutions":[{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Regina Barzilay","raw_affiliation_strings":["MIT CSAIL","MIT Jameel Clinic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MIT CSAIL","institution_ids":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]},{"raw_affiliation_string":"MIT Jameel Clinic","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":688,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.9789999723434448,"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":0.9789999723434448,"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":0.013399999588727951,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0015999999595806003,"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/boltz-2","display_name":"Boltz-2","score":0.9800000190734863},{"id":"https://openalex.org/keywords/binding-affinity-prediction","display_name":"binding affinity prediction","score":0.9549999833106995},{"id":"https://openalex.org/keywords/free-energy-perturbation","display_name":"free energy perturbation","score":0.6850000023841858},{"id":"https://openalex.org/keywords/foundation-models","display_name":"foundation models","score":0.6000000238418579},{"id":"https://openalex.org/keywords/distance-constraints","display_name":"distance constraints","score":0.871999979019165},{"id":"https://openalex.org/keywords/tyk2","display_name":"TYK2","score":0.9459999799728394},{"id":"https://openalex.org/keywords/computational-efficiency","display_name":"computational efficiency","score":0.5789999961853027}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35230666399002075},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33859872817993164},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33056640625},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3253262937068939},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.32226306200027466},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14132559299468994}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1101/2025.06.14.659707","doi":"https://doi.org/10.1101/2025.06.14.659707","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.06.14.659707","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:40667369","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40667369","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,"listed_in":[],"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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12262699","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12262699","pdf_url":null,"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,"listed_in":[],"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":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1101/2025.06.14.659707","doi":"https://doi.org/10.1101/2025.06.14.659707","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.06.14.659707","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1810876930","display_name":"Graduate Training in Computational and Systems Biology","funder_award_id":"T32GM087237","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5807165219","display_name":"MATCHMAKERS - Creating and training AI tools for TCR binding prediction and design","funder_award_id":"1ot2ca297463-01","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":58,"referenced_works":["https://openalex.org/W1928213240","https://openalex.org/W1968984443","https://openalex.org/W1985588649","https://openalex.org/W2016370660","https://openalex.org/W2043509228","https://openalex.org/W2061583504","https://openalex.org/W2096864392","https://openalex.org/W2114162221","https://openalex.org/W2154670681","https://openalex.org/W2303521084","https://openalex.org/W2346422904","https://openalex.org/W2578240541","https://openalex.org/W2610903912","https://openalex.org/W2911872747","https://openalex.org/W2914542247","https://openalex.org/W2950954328","https://openalex.org/W3034675470","https://openalex.org/W3082081167","https://openalex.org/W3093634533","https://openalex.org/W3094553402","https://openalex.org/W3100348855","https://openalex.org/W3168451642","https://openalex.org/W3211795435","https://openalex.org/W4205171481","https://openalex.org/W4220887735","https://openalex.org/W4220974185","https://openalex.org/W4281790889","https://openalex.org/W4291624945","https://openalex.org/W4297914802","https://openalex.org/W4307468223","https://openalex.org/W4311860580","https://openalex.org/W4323812845","https://openalex.org/W4365504163","https://openalex.org/W4366465619","https://openalex.org/W4376129086","https://openalex.org/W4377968247","https://openalex.org/W4387440676","https://openalex.org/W4387639561","https://openalex.org/W4388455891","https://openalex.org/W4388870515","https://openalex.org/W4389068621","https://openalex.org/W4389721329","https://openalex.org/W4391673325","https://openalex.org/W4392093325","https://openalex.org/W4392500218","https://openalex.org/W4395447845","https://openalex.org/W4396721167","https://openalex.org/W4399781535","https://openalex.org/W4403013573","https://openalex.org/W4404511368","https://openalex.org/W4404565424","https://openalex.org/W4404826794","https://openalex.org/W4410552412","https://openalex.org/W4412165572","https://openalex.org/W4413739329","https://openalex.org/W4414822341","https://openalex.org/W6894265192","https://openalex.org/W7133233884"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"Accurately":[0],"modeling":[1],"biomolecular":[2,26],"interactions":[3],"is":[4],"a":[5,38,51,133,185,190],"central":[6],"challenge":[7],"in":[8,34,102],"modern":[9],"biology.":[10],"While":[11],"recent":[12],"advances,":[13],"such":[14],"as":[15,150],"AlphaFold3":[16],"and":[17,44,64,77,84,164,173,181,192,198],"Boltz-1,":[18],"have":[19],"substantially":[20],"improved":[21],"our":[22,87],"ability":[23],"to":[24,86,93,144],"predict":[25],"complex":[27],"structures,":[28],"these":[29],"models":[30],"still":[31],"fall":[32],"short":[33],"predicting":[35],"binding":[36,106],"affinity,":[37],"critical":[39],"property":[40],"underlying":[41],"molecular":[42],"function":[43],"therapeutic":[45],"efficacy.":[46],"Here,":[47],"we":[48,139,175],"present":[49],"Boltz-2,":[50],"new":[52],"structural":[53],"biology":[54],"foundation":[55,194],"model":[56,92,135],"that":[57],"exhibits":[58],"strong":[59,111],"performance":[60,96],"for":[61,81,136,195],"both":[62,196],"structure":[63,82],"affinity":[65],"prediction.":[66],"Boltz-2":[67,131,178],"introduces":[68],"controllability":[69],"features":[70],"including":[71],"experimental":[72,114],"method":[73],"conditioning,":[74],"distance":[75],"constraints,":[76],"multi-chain":[78],"template":[79],"integration":[80],"prediction,":[83],"is,":[85],"knowledge,":[88],"the":[89,95,157,168],"first":[90],"AI":[91],"approach":[94],"of":[97,170],"free-energy":[98],"perturbation":[99],"(FEP)":[100],"methods":[101],"estimating":[103],"small":[104,137],"molecule-protein":[105],"affinity.":[107],"Crucially,":[108],"it":[109],"achieves":[110],"correlation":[112],"with":[113,132],"readouts":[115],"on":[116,156],"many":[117],"benchmarks,":[118],"while":[119],"being":[120],"at":[121,167],"least":[122],"1000\u00d7":[123],"more":[124],"computationally":[125],"efficient":[126],"than":[127],"FEP.":[128],"By":[129],"coupling":[130],"generative":[134],"molecules,":[138],"demonstrate":[140],"an":[141],"effective":[142],"workflow":[143],"find":[145],"diverse,":[146],"synthesizable,":[147],"high-affinity":[148],"binders,":[149],"estimated":[151],"by":[152],"absolute":[153],"FEP":[154],"simulations":[155],"TYK2":[158],"target.":[159],"To":[160],"foster":[161],"broad":[162],"adoption":[163],"further":[165],"innovation":[166],"intersection":[169],"machine":[171],"learning":[172],"biology,":[174],"are":[176],"releasing":[177],"weights,":[179],"inference,":[180],"training":[182],"code":[183],"under":[184],"permissive":[186],"open":[187],"license,":[188],"providing":[189],"robust":[191],"extensible":[193],"academic":[197],"industrial":[199],"research.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":561},{"year":2025,"cited_by_count":127}],"updated_date":"2026-10-22T09:42:04.148104","created_date":"2025-10-10T00:00:00"}