{"id":"https://openalex.org/W7204140035","doi":"https://doi.org/10.1093/bioinformatics/btag489","title":"PreFold-dG: estimating binding affinity of protein\u2013protein interaction from intermediate representations of protein folding model","display_name":"PreFold-dG: estimating binding affinity of protein\u2013protein interaction from intermediate representations of protein folding model","publication_year":2026,"publication_date":"2026-07-01","ids":{"openalex":"https://openalex.org/W7204140035","doi":"https://doi.org/10.1093/bioinformatics/btag489","pmid":"https://pubmed.ncbi.nlm.nih.gov/42635209","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13501319"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag489","doi":"https://doi.org/10.1093/bioinformatics/btag489","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag489","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag489","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030619424","display_name":"S. J. Park","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405258446","display_name":"LG AI Research (South Korea)","ror":"https://ror.org/00nt82y31","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210131320","https://openalex.org/I4405258446"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Sungjoon Park","raw_affiliation_strings":["Bio Intelligence Lab, LG AI Research , Seoul, 07789,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bio Intelligence Lab, LG AI Research , Seoul, 07789,","institution_ids":["https://openalex.org/I4405258446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084415297","display_name":"Soorin Yim","orcid":"https://orcid.org/0000-0001-5379-3196","observed_orcids":["https://orcid.org/0000-0001-5379-3196"]},"institutions":[{"id":"https://openalex.org/I4405258446","display_name":"LG AI Research (South Korea)","ror":"https://ror.org/00nt82y31","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210131320","https://openalex.org/I4405258446"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Soorin Yim","raw_affiliation_strings":["Bio Intelligence Lab, LG AI Research , Seoul, 07789,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bio Intelligence Lab, LG AI Research , Seoul, 07789,","institution_ids":["https://openalex.org/I4405258446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5148029706","display_name":"Dongyun Kim","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]},{"id":"https://openalex.org/I4405258446","display_name":"LG AI Research (South Korea)","ror":"https://ror.org/00nt82y31","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210131320","https://openalex.org/I4405258446"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Dongyun Kim","raw_affiliation_strings":["Bio Intelligence Lab, LG AI Research , Seoul, 07789,","School of Biological Science, Seoul National University , Seoul, 08826,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bio Intelligence Lab, LG AI Research , Seoul, 07789,","institution_ids":["https://openalex.org/I4405258446"]},{"raw_affiliation_string":"School of Biological Science, Seoul National University , Seoul, 08826,","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5147982288","display_name":"Kiwoong Yoo","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405258446","display_name":"LG AI Research (South Korea)","ror":"https://ror.org/00nt82y31","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210131320","https://openalex.org/I4405258446"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kiwoong Yoo","raw_affiliation_strings":["Bio Intelligence Lab, LG AI Research , Seoul, 07789,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bio Intelligence Lab, LG AI Research , Seoul, 07789,","institution_ids":["https://openalex.org/I4405258446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5145277981","display_name":"Doyeong Hwang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405258446","display_name":"LG AI Research (South Korea)","ror":"https://ror.org/00nt82y31","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210131320","https://openalex.org/I4405258446"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Doyeong Hwang","raw_affiliation_strings":["Bio Intelligence Lab, LG AI Research , Seoul, 07789,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bio Intelligence Lab, LG AI Research , Seoul, 07789,","institution_ids":["https://openalex.org/I4405258446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5147948394","display_name":"Kyungwook Lee","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405258446","display_name":"LG AI Research (South Korea)","ror":"https://ror.org/00nt82y31","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210131320","https://openalex.org/I4405258446"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Kyungwook Lee","raw_affiliation_strings":["Bio Intelligence Lab, LG AI Research , Seoul, 07789,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bio Intelligence Lab, LG AI Research , Seoul, 07789,","institution_ids":["https://openalex.org/I4405258446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101431618","display_name":"Jongseong Jang","orcid":"https://orcid.org/0000-0001-6556-0365","observed_orcids":["https://orcid.org/0000-0001-6556-0365"]},"institutions":[{"id":"https://openalex.org/I4405258446","display_name":"LG AI Research (South Korea)","ror":"https://ror.org/00nt82y31","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210131320","https://openalex.org/I4405258446"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jongseong Jang","raw_affiliation_strings":["Bio Intelligence Lab, LG AI Research , Seoul, 07789,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bio Intelligence Lab, LG AI Research , Seoul, 07789,","institution_ids":["https://openalex.org/I4405258446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5121064654","display_name":"Kiyoung Kim","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405258446","display_name":"LG AI Research (South Korea)","ror":"https://ror.org/00nt82y31","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210131320","https://openalex.org/I4405258446"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Kiyoung Kim","raw_affiliation_strings":["Bio Intelligence Lab, LG AI Research , Seoul, 07789,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bio Intelligence Lab, LG AI Research , Seoul, 07789,","institution_ids":["https://openalex.org/I4405258446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5121064654"],"corresponding_institution_ids":["https://openalex.org/I4405258446"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"Supplement_2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9384999871253967,"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":0.9384999871253967,"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":0.04479999840259552,"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":0.004800000227987766,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/boltz-2","display_name":"Boltz-2","score":0.8259999752044678},{"id":"https://openalex.org/keywords/protein-complexes","display_name":"protein complexes","score":0.4950000047683716},{"id":"https://openalex.org/keywords/intermediate-representation","display_name":"intermediate representation","score":0.5080000162124634},{"id":"https://openalex.org/keywords/broadly-neutralizing-antibodies","display_name":"broadly neutralizing antibodies","score":0.7450000047683716}],"concepts":[{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.7580000162124634},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.6004999876022339},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.5138999819755554},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5062999725341797},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47850000858306885},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.46160000562667847},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.450300008058548},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.43650001287460327},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.421999990940094},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4052000045776367},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.3995000123977661},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.3977000117301941},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.39500001072883606},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.38670000433921814},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.38449999690055847},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.37720000743865967},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.31139999628067017},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.30329999327659607},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29840001463890076},{"id":"https://openalex.org/C2780430158","wikidata":"https://www.wikidata.org/wiki/Q7685902","display_name":"Target protein","level":3,"score":0.2809999883174896},{"id":"https://openalex.org/C25166345","wikidata":"https://www.wikidata.org/wiki/Q4914012","display_name":"Binding domain","level":3,"score":0.2750999927520752},{"id":"https://openalex.org/C2988375501","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein stability","level":2,"score":0.26899999380111694},{"id":"https://openalex.org/C178910836","wikidata":"https://www.wikidata.org/wiki/Q2196961","display_name":"Molecular model","level":2,"score":0.2678999900817871},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2669999897480011},{"id":"https://openalex.org/C191120209","wikidata":"https://www.wikidata.org/wiki/Q908902","display_name":"Structural biology","level":2,"score":0.2630000114440918},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.26170000433921814},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.2547999918460846},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.25099998712539673}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag489","doi":"https://doi.org/10.1093/bioinformatics/btag489","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag489","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42635209","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42635209","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":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13501319","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13501319/","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag489","doi":"https://doi.org/10.1093/bioinformatics/btag489","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag489","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2082922089","display_name":null,"funder_award_id":"RS-2025\u201325442149","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"}],"funders":[{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W2780523853","https://openalex.org/W2920817727","https://openalex.org/W2953103783","https://openalex.org/W3045100294","https://openalex.org/W3177828909","https://openalex.org/W3198724845","https://openalex.org/W4229331784","https://openalex.org/W4396721167","https://openalex.org/W4400313991","https://openalex.org/W4402322935","https://openalex.org/W4408220597","https://openalex.org/W4408468118","https://openalex.org/W4411175534","https://openalex.org/W4411463597","https://openalex.org/W4412454131","https://openalex.org/W4414997250"],"related_works":["https://openalex.org/W4414738646","https://openalex.org/W7202353319","https://openalex.org/W4403565998","https://openalex.org/W4409218613","https://openalex.org/W7164763516","https://openalex.org/W2909255640","https://openalex.org/W7111181770","https://openalex.org/W7147177875","https://openalex.org/W4410233685","https://openalex.org/W2512372054"],"abstract_inverted_index":{"MOTIVATION:":[0],"Binding":[1],"affinity":[2,46,51,103,162],"governs":[3],"how":[4],"proteins":[5],"interact":[6],"and":[7,19,146,165,190],"underlies":[8],"essential":[9],"biological":[10],"processes.":[11],"Computational":[12],"approaches":[13],"have":[14,73],"been":[15],"developed":[16],"to":[17,58,106,187],"simulate":[18],"predict":[20],"protein":[21,70,78,122,134],"binding,":[22],"but":[23],"the":[24,63,182],"scarcity":[25],"of":[26,65,77,101,121],"high-quality":[27],"data":[28,60,206],"has":[29,104],"imposed":[30],"significant":[31],"constraints.":[32],"One":[33],"consequence":[34],"is":[35],"that":[36,117,175],"most":[37],"methods":[38],"focus":[39],"on":[40,159,168,201],"predicting":[41],"mutational":[42],"changes":[43],"in":[44,69,80,181],"binding":[45,50,88,102,119,161],"(\u0394\u0394G),":[47],"rather":[48,150],"than":[49,151],"(\u0394G)":[52],"itself.":[53],"This":[54],"practice":[55],"risks":[56],"overfitting":[57],"skewed":[59],"distributions,":[61],"limiting":[62],"generalizability":[64],"predictions.":[66,110],"Recent":[67],"advances":[68,97],"structure":[71,135],"prediction":[72,100,163],"enabled":[74],"computational":[75],"modeling":[76,188],"conformations":[79],"mass,":[81],"providing":[82],"rich":[83],"structural":[84],"information":[85,141],"from":[86,127],"which":[87],"interactions":[89],"can":[90],"be":[91],"largely":[92],"explained.":[93],"However,":[94],"leveraging":[95],"these":[96],"for":[98,133],"effective":[99],"yet":[105],"translate":[107],"into":[108],"reliable":[109],"RESULTS:":[111],"We":[112,193],"present":[113],"PreFold-dG,":[114],"a":[115],"model":[116,132,197],"estimates":[118],"affinities":[120],"complexes":[123],"utilizing":[124],"intermediate":[125,177],"embeddings":[126,178],"Boltz-2,":[128],"an":[129],"open-source":[130],"foundation":[131],"prediction.":[136],"Our":[137],"approach":[138],"aggregates":[139],"residue-level":[140],"weighted":[142],"by":[143],"interresidue":[144],"distance,":[145],"predicts":[147],"\u0394G":[148,191],"directly":[149],"its":[152],"derivative,":[153],"\u0394\u0394G.":[154],"PreFold-dG":[155],"achieved":[156],"state-of-the-art":[157],"performance":[158],"well-established":[160],"benchmarks":[164],"demonstrated":[166],"robustness":[167],"independent":[169],"test":[170],"sets.":[171],"Ablation":[172],"studies":[173,200],"suggest":[174],"all":[176],"are":[179],"utilized":[180],"prediction,":[183],"whereas":[184],"their":[185],"contributions":[186],"\u0394\u0394G":[189],"vary.":[192],"further":[194],"validated":[195],"our":[196],"through":[198],"case":[199],"real-world":[202],"broadly":[203],"neutralizing":[204],"antibody":[205],"with":[207],"evolutionary":[208],"relevance.":[209],"AVAILABILITY:":[210],"https://github.com/LGAI-Research/PreFold-dG.":[211]},"counts_by_year":[],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2026-08-25T00:00:00"}
