{"id":"https://openalex.org/W7225402889","doi":"https://doi.org/10.64898/2026.11.04.764332","title":"RPFace: From biased structural benchmarks to generalizable RNA-protein interface prediction","display_name":"RPFace: From biased structural benchmarks to generalizable RNA-protein interface prediction","publication_year":2026,"publication_date":"2026-11-06","ids":{"openalex":"https://openalex.org/W7225402889","doi":"https://doi.org/10.64898/2026.11.04.764332"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.04.764332","doi":"https://doi.org/10.64898/2026.11.04.764332","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.04.764332","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.04.764332.full.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.04.764332.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116573635","display_name":"Helyasadat Hashemi Aghdam","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Helyasadat Hashemi Aghdam","raw_affiliation_strings":["Bilkent University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bilkent University","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114475334","display_name":"Sobhan Shukueian Tabrizi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Sobhan Shukueian Tabrizi","raw_affiliation_strings":["Bilkent University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bilkent University","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090836372","display_name":"A. Erc\u00fcment \u00c7i\u00e7ek","orcid":"https://orcid.org/0000-0001-8613-6619","observed_orcids":["https://orcid.org/0000-0001-8613-6619"]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"A. Ercument Cicek","raw_affiliation_strings":["Bilkent University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bilkent University","institution_ids":["https://openalex.org/I168864056"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5090836372"],"corresponding_institution_ids":["https://openalex.org/I168864056"],"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.8955000042915344,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.8955000042915344,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.07999999821186066,"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/T10604","display_name":"RNA Research and Splicing","score":0.01080000028014183,"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/benchmark-bias","display_name":"benchmark bias","score":0.6539999842643738},{"id":"https://openalex.org/keywords/generalization","display_name":"generalization","score":0.6430000066757202},{"id":"https://openalex.org/keywords/co-folding","display_name":"co-folding","score":0.765999972820282},{"id":"https://openalex.org/keywords/molecular-docking","display_name":"molecular docking","score":0.7459999918937683},{"id":"https://openalex.org/keywords/ribosomal-complexes","display_name":"ribosomal complexes","score":0.7799999713897705},{"id":"https://openalex.org/keywords/rna-secondary-structure-prediction","display_name":"RNA secondary structure prediction","score":0.6179999709129333},{"id":"https://openalex.org/keywords/multimodal-embeddings","display_name":"multimodal embeddings","score":0.4740000069141388},{"id":"https://openalex.org/keywords/zero-shot-prediction","display_name":"zero-shot prediction","score":0.703000009059906},{"id":"https://openalex.org/keywords/sequence-based-prediction","display_name":"sequence-based prediction","score":0.5230000019073486},{"id":"https://openalex.org/keywords/conformational-change","display_name":"conformational change","score":0.718999981880188}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6155999898910522},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.5501999855041504},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.51910001039505},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.44609999656677246},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4293999969959259},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.4138000011444092},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38769999146461487},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37959998846054077},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3652999997138977},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.3411000072956085},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.33869999647140503},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3296999931335449},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3052999973297119},{"id":"https://openalex.org/C126142528","wikidata":"https://www.wikidata.org/wiki/Q3771876","display_name":"Nucleic acid structure","level":4,"score":0.3050999939441681},{"id":"https://openalex.org/C2779714256","wikidata":"https://www.wikidata.org/wiki/Q25305062","display_name":"Multiple Models","level":2,"score":0.29760000109672546},{"id":"https://openalex.org/C4679612","wikidata":"https://www.wikidata.org/wiki/Q866298","display_name":"Aggregate (composite)","level":2,"score":0.28839999437332153},{"id":"https://openalex.org/C2777936996","wikidata":"https://www.wikidata.org/wiki/Q17148461","display_name":"Conformational ensembles","level":3,"score":0.2827000021934509},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2703000009059906},{"id":"https://openalex.org/C67905577","wikidata":"https://www.wikidata.org/wiki/Q215980","display_name":"Ribosomal RNA","level":3,"score":0.2583000063896179}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.04.764332","doi":"https://doi.org/10.64898/2026.11.04.764332","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.04.764332","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.04.764332.full.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.04.764332","doi":"https://doi.org/10.64898/2026.11.04.764332","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.04.764332","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/06/2026.11.04.764332.full.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225402889.pdf","grobid_xml":"https://content.openalex.org/works/W7225402889.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W4290546063","https://openalex.org/W4411463597","https://openalex.org/W4416985807"],"related_works":["https://openalex.org/W7155559116","https://openalex.org/W7203724449","https://openalex.org/W1994183585","https://openalex.org/W7225306298","https://openalex.org/W4321784037","https://openalex.org/W2600989574","https://openalex.org/W7157897872","https://openalex.org/W2124432783","https://openalex.org/W2768702322","https://openalex.org/W2116498086"],"abstract_inverted_index":{"Modeling":[0],"protein-RNA":[1,68],"complexes":[2,105],"with":[3,109,202,263,273],"co-folding":[4,99],"and":[5,61,73,106,133,178,214,226,235,243,267,288],"docking":[6,116],"methods":[7,12,100,143,259],"is":[8,101,119,135,222,238],"routine,":[9],"yet":[10],"these":[11],"are":[13,126,290],"evaluated":[14],"on":[15,23,44,260,270],"benchmarks":[16],"whose":[17],"composition":[18],"mirrors":[19],"the":[20,42,45,49,52,56,95,123,130,160,165,171,257,274],"deposited":[21],"structures":[22,201],"which":[24],"they":[25],"were":[26],"trained":[27],"or":[28,190],"tuned,":[29],"leaving":[30],"open":[31],"whether":[32],"their":[33],"reported":[34],"performance":[35,232],"reflects":[36],"true":[37],"generalization.":[38],"Here,":[39],"we":[40,59,89,156],"focus":[41],"evaluation":[43],"region":[46],"that":[47,66,91,168,207,229],"carries":[48],"biological":[50],"signal:":[51],"binding":[53,96,172],"interface.":[54],"For":[55,115],"first":[57,166],"time,":[58],"construct":[60],"release":[62],"a":[63,77,203,223,253],"fair":[64],"benchmark":[65],"stratifies":[67],"data":[69,289],"into":[70],"distinct":[71],"structural":[72,234],"experimental":[74,113,187,236],"groups,":[75],"providing":[76],"more":[78],"stringent":[79],"test":[80],"of":[81,93,142,162,174,198],"generalization":[82],"than":[83],"aggregate":[84],"averages.":[85],"On":[86],"this":[87,154],"benchmark,":[88],"find":[90],"accuracy":[92],"detecting":[94],"site":[97],"using":[98,281],"concentrated":[102],"in":[103,148,246,277],"ribosomal":[104],"varies":[107],"systematically":[108],"factors":[110],"such":[111],"as":[112],"modality.":[114],"methods,":[117],"it":[118,134,221],"reliable":[120],"only":[121,282],"when":[122],"input":[124],"conformations":[125],"already":[127],"close":[128],"to":[129,145,147,159,240,245],"bound":[131],"state,":[132],"inconsistent":[136],"across":[137,233],"RNA":[138,180,211,271],"classes.":[139],"Both":[140],"families":[141],"fail":[144],"transfer":[146],"vivo":[149,247],"CLIP":[150],"experiments.":[151],"To":[152],"address":[153],"gap,":[155],"introduce":[157],"RPFace,":[158],"best":[161],"our":[163],"knowledge":[164],"model":[167,228],"jointly":[169],"predicts":[170],"preference":[173],"every":[175,179],"protein":[176,261],"residue":[177],"nucleotide":[181],"directly":[182],"from":[183,210],"sequence,":[184],"requiring":[185],"no":[186,264],"structure,":[188],"template,":[189],"multiple":[191],"sequence":[192,283],"alignment.":[193],"RPFace":[194,255],"combines":[195],"an":[196],"ensemble":[197],"predicted":[199],"secondary":[200],"multi-modal":[204],"embedding-enrichment":[205],"scheme":[206],"fuses":[208],"representations":[209],"foundation":[212],"models":[213],"structure":[215],"prediction":[216],"models.":[217],"Unlike":[218],"existing":[219],"approaches,":[220],"very":[224],"small":[225],"fast":[227],"delivers":[230],"stable":[231],"conditions,":[237],"robust":[239],"conformational":[241],"change,":[242],"generalizes":[244],"datasets":[248],"without":[249],"extensive":[250],"pretraining.":[251],"As":[252],"result,":[254],"matches":[256],"state-of-the-art":[258],"interfaces":[262],"evolutionary":[265],"information,":[266],"outperforms":[268],"them":[269],"interfaces,":[272],"largest":[275],"gains":[276],"zero-shot":[278],"settings":[279],"despite":[280],"information.":[284],"The":[285],"model,":[286],"code,":[287],"available":[291],"at":[292],"Github.":[293]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-11-07T00:00:00"}