{"id":"https://openalex.org/W7215945686","doi":"https://doi.org/10.48550/arxiv.2610.00191","title":"Improving scoring functions for protein-protein docking with LambdaLoss","display_name":"Improving scoring functions for protein-protein docking with LambdaLoss","publication_year":2026,"publication_date":"2026-09-18","ids":{"openalex":"https://openalex.org/W7215945686","doi":"https://doi.org/10.48550/arxiv.2610.00191"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2610.00191","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.00191","pdf_url":"https://arxiv.org/pdf/2610.00191","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2610.00191","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5156178401","display_name":"Richard Zhu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhu, Richard","raw_affiliation_strings":["Department of Statistics Harvard University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics Harvard University","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088684708","display_name":"Darren Xu","orcid":"https://orcid.org/0000-0002-3879-039X","observed_orcids":["https://orcid.org/0000-0002-3879-039X"]},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xu, Darren","raw_affiliation_strings":["Department of Chemical and Biomolecular Engineering Johns Hopkins University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering Johns Hopkins University","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063532782","display_name":"Lee\u2010Shin Chu","orcid":"https://orcid.org/0000-0001-8315-642X","observed_orcids":["https://orcid.org/0000-0001-8315-642X"]},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chu, Lee-Shin","raw_affiliation_strings":["Department of Chemical and Biomolecular Engineering Johns Hopkins University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering Johns Hopkins University","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009383312","display_name":"Jeffrey J. Gray","orcid":"https://orcid.org/0000-0001-6380-2324","observed_orcids":["https://orcid.org/0000-0001-6380-2324"]},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gray, Jeffrey J.","raw_affiliation_strings":["Department of Chemical and Biomolecular Engineering Johns Hopkins University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering Johns Hopkins University","institution_ids":["https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9336000084877014,"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":0.9336000084877014,"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":0.03689999878406525,"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"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.014999999664723873,"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/protein-protein-docking","display_name":"protein-protein docking","score":0.996999979019165},{"id":"https://openalex.org/keywords/scoring-functions","display_name":"scoring functions","score":0.8889999985694885},{"id":"https://openalex.org/keywords/learning-to-rank","display_name":"learning to rank","score":0.9129999876022339},{"id":"https://openalex.org/keywords/pose-ranking","display_name":"pose ranking","score":0.9350000023841858},{"id":"https://openalex.org/keywords/immune-complexes","display_name":"immune complexes","score":0.8930000066757202}],"concepts":[{"id":"https://openalex.org/C2779179475","wikidata":"https://www.wikidata.org/wiki/Q3545649","display_name":"Decoy","level":3,"score":0.8269000053405762},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.7361000180244446},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6801999807357788},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5683000087738037},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5378000140190125},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.501800000667572},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.4726000130176544},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4375},{"id":"https://openalex.org/C169903167","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Test set","level":2,"score":0.35019999742507935},{"id":"https://openalex.org/C65660741","wikidata":"https://www.wikidata.org/wiki/Q3952743","display_name":"Score","level":2,"score":0.3248000144958496},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.31200000643730164},{"id":"https://openalex.org/C12725497","wikidata":"https://www.wikidata.org/wiki/Q810247","display_name":"Baseline (sea)","level":2,"score":0.2741999924182892},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.2531000077724457},{"id":"https://openalex.org/C86037889","wikidata":"https://www.wikidata.org/wiki/Q4330127","display_name":"Learning to rank","level":3,"score":0.25189998745918274}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2610.00191","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.00191","pdf_url":"https://arxiv.org/pdf/2610.00191","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2610.00191","doi":"https://doi.org/10.48550/arxiv.2610.00191","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2610.00191","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2610.00191","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2610.00191","pdf_url":"https://arxiv.org/pdf/2610.00191","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G541412426","display_name":"REU Site: A Cyberlinked Program in Computational Biomolecular Structure & Design","funder_award_id":"2244288","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G9000885060","display_name":"Prediction of the Structures of Protein Complexes","funder_award_id":"R35GM141881","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310145","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95"},{"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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7215945686.pdf","grobid_xml":"https://content.openalex.org/works/W7215945686.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W186258178","https://openalex.org/W1030883578","https://openalex.org/W1907442748","https://openalex.org/W2018410079","https://openalex.org/W2149427297","https://openalex.org/W2508425869","https://openalex.org/W2898073868","https://openalex.org/W2970009611","https://openalex.org/W3171236517","https://openalex.org/W3185671814","https://openalex.org/W4364382221","https://openalex.org/W4386495900","https://openalex.org/W4389568864","https://openalex.org/W4396721167","https://openalex.org/W4403680155","https://openalex.org/W4406699368","https://openalex.org/W4411463597","https://openalex.org/W4413138209","https://openalex.org/W7196941264","https://openalex.org/W7204084455"],"related_works":["https://openalex.org/W4403680155","https://openalex.org/W2100025509","https://openalex.org/W2071957747","https://openalex.org/W7155101381","https://openalex.org/W2060444292","https://openalex.org/W4406699368","https://openalex.org/W2285983121","https://openalex.org/W2420141398","https://openalex.org/W1985210344","https://openalex.org/W7100370983"],"abstract_inverted_index":{"Modeling":[0],"protein-protein":[1,15,32,121],"interactions":[2],"requires":[3],"accurate":[4],"scoring":[5,117],"functions":[6],"that":[7],"can":[8],"rank":[9],"potential":[10],"poses":[11,20,71,95],"(conformations)":[12],"of":[13,59,68],"a":[14,27,105],"complex":[16],"to":[17,103],"differentiate":[18],"near-native":[19],"from":[21,45,73,79],"incorrect":[22],"ones.":[23],"Here,":[24],"we":[25],"propose":[26],"general":[28],"framework":[29,52],"for":[30,116],"improving":[31],"pose":[33],"ranking":[34,87,114],"and":[35,99,120],"other":[36],"biomolecular":[37],"interaction":[38],"models":[39],"using":[40],"the":[41,46,55,62,74,80],"LambdaLoss":[42,63],"loss":[43],"function":[44],"Learning-to-Rank":[47],"field.":[48],"We":[49],"test":[50],"this":[51],"by":[53],"fine-tuning":[54],"energy":[56],"prediction":[57],"head":[58],"DFMDock":[60,113],"with":[61,123],"on":[64],"an":[65],"augmented":[66],"dataset":[67],"2.9M":[69],"decoy":[70],"derived":[72],"DIPS":[75],"dataset.":[76],"On":[77],"targets":[78],"CAPRI":[81],"score":[82],"set":[83],"benchmark,":[84],"our":[85],"fine-tuned":[86],"model":[88],"LambdaDockScore":[89,108],"is":[90],"better":[91],"at":[92],"identifying":[93],"correct":[94],"in":[96],"its":[97],"top-1":[98],"top-5":[100],"predictions":[101],"compared":[102],"EuDockScore,":[104],"state-of-the-art":[106],"method.":[107],"also":[109],"improves":[110],"upon":[111],"baseline":[112],"performance":[115],"antibody-antigen":[118],"complexes":[119,122],"very":[124],"large":[125],"or":[126],"small":[127],"binding":[128],"interfaces.":[129]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-10-03T00:00:00"}
