{"id":"https://openalex.org/W7157897872","doi":"https://doi.org/10.1093/bioinformatics/btag202","title":"Inferring the qualities of protein\u2013RNA models with graph transformers","display_name":"Inferring the qualities of protein\u2013RNA models with graph transformers","publication_year":2026,"publication_date":"2026-04-22","ids":{"openalex":"https://openalex.org/W7157897872","doi":"https://doi.org/10.1093/bioinformatics/btag202","pmid":"https://pubmed.ncbi.nlm.nih.gov/42048142"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag202","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag202","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,"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"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag202","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109840098","display_name":"A. Siciliano","orcid":null},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew Jordan Siciliano","raw_affiliation_strings":["Department of Computer Science, University of Miami , Coral Gables, FL 33124,"],"raw_orcid":"https://orcid.org/0009-0007-1464-3583","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Miami , Coral Gables, FL 33124,","institution_ids":["https://openalex.org/I145608581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101797011","display_name":"Yifan Bao","orcid":"https://orcid.org/0000-0003-0460-9326"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yifan Bao","raw_affiliation_strings":["Department of Computer Science, University of Miami , Coral Gables, FL 33124,"],"raw_orcid":"https://orcid.org/0009-0008-9157-3440","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Miami , Coral Gables, FL 33124,","institution_ids":["https://openalex.org/I145608581"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000944013","display_name":"Bishal Shrestha","orcid":"https://orcid.org/0009-0004-8330-4348"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bishal Shrestha","raw_affiliation_strings":["Department of Computer Science, University of Miami , Coral Gables, FL 33124,"],"raw_orcid":"https://orcid.org/0009-0004-8330-4348","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Miami , Coral Gables, FL 33124,","institution_ids":["https://openalex.org/I145608581"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5134856272","display_name":"Zheng Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zheng Wang","raw_affiliation_strings":["Department of Computer Science, University of Miami , Coral Gables, FL 33124,"],"raw_orcid":"https://orcid.org/0000-0003-3892-6151","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Miami , Coral Gables, FL 33124,","institution_ids":["https://openalex.org/I145608581"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5134856272"],"corresponding_institution_ids":["https://openalex.org/I145608581"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.54085325,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.3343000113964081,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.3343000113964081,"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":0.1899999976158142,"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":0.1185000017285347,"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/graph","display_name":"Graph","score":0.5189999938011169},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4487999975681305},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.44290000200271606},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.38429999351501465},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.38199999928474426},{"id":"https://openalex.org/keywords/data-quality","display_name":"Data quality","score":0.37139999866485596}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6098999977111816},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5189999938011169},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4853000044822693},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4487999975681305},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.44290000200271606},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42080000042915344},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40549999475479126},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.38429999351501465},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.38199999928474426},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.37139999866485596},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.3407999873161316},{"id":"https://openalex.org/C2778891732","wikidata":"https://www.wikidata.org/wiki/Q2751223","display_name":"Carp","level":3,"score":0.32659998536109924},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.322299987077713},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.30709999799728394},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.2992999851703644},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.2976999878883362},{"id":"https://openalex.org/C109747225","wikidata":"https://www.wikidata.org/wiki/Q815758","display_name":"Scarcity","level":2,"score":0.2565999925136566}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016601","descriptor_name":"RNA-Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062105","descriptor_name":"Molecular Docking Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag202","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag202","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,"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:42048142","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42048142","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:13189855","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13189855/","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,"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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag202","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag202","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,"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":[],"awards":[{"id":"https://openalex.org/G7826479737","display_name":null,"funder_award_id":"1R35GM137974","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W142718297","https://openalex.org/W1984574291","https://openalex.org/W2008708467","https://openalex.org/W2055317682","https://openalex.org/W2075200002","https://openalex.org/W2081724853","https://openalex.org/W2089652064","https://openalex.org/W2091705944","https://openalex.org/W2129279466","https://openalex.org/W2134489577","https://openalex.org/W2149605074","https://openalex.org/W2151581834","https://openalex.org/W2597602671","https://openalex.org/W2900416129","https://openalex.org/W2917724292","https://openalex.org/W2920949012","https://openalex.org/W2950954328","https://openalex.org/W3016982165","https://openalex.org/W3034567160","https://openalex.org/W3043664941","https://openalex.org/W3177828909","https://openalex.org/W3187966659","https://openalex.org/W3211811754","https://openalex.org/W4281790889","https://openalex.org/W4281993476","https://openalex.org/W4293475204","https://openalex.org/W4309862248","https://openalex.org/W4321784037","https://openalex.org/W4385075189","https://openalex.org/W4387798438","https://openalex.org/W4396721167","https://openalex.org/W4403039940","https://openalex.org/W4404246274","https://openalex.org/W4406038928","https://openalex.org/W4415699195"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Breakthrough":[1],"advancements":[2],"in":[3,84,125,231],"protein":[4,108],"tertiary":[5],"and":[6,16,33,45,51,55,67,107,136,167,193,201,228],"quaternary":[7],"structure":[8,38],"prediction":[9],"have":[10],"accelerated":[11],"structural":[12,90],"bioinformatics":[13,91],"research":[14],"activity":[15],"drug":[17],"development":[18],"processes.":[19],"However,":[20],"many":[21],"biological":[22,68],"mechanisms":[23],"involve":[24],"more":[25],"complicated":[26],"interactions,":[27],"such":[28],"as":[29],"those":[30],"between":[31],"amino":[32],"nucleic":[34],"acids.":[35],"Predicting":[36],"the":[37,160,169,206],"of":[39,88,105,115,159],"protein-RNA":[40,77,89,116,122,146,195,214],"complexes":[41],"is":[42,241],"highly":[43],"relevant":[44],"challenging":[46],"due":[47],"to":[48,110,156,181,224],"data":[49],"scarcity":[50],"experimental":[52],"difficulties.":[53],"Understanding":[54],"interpreting":[56],"these":[57],"interactions":[58],"can":[59,80],"yield":[60],"crucial":[61],"insights":[62],"into":[63],"various":[64],"human":[65],"diseases":[66],"phenomena.":[69],"Thus,":[70],"quality":[71,103,113,139,171,178,234],"assessment":[72,104],"methods":[73,150],"that":[74],"specifically":[75],"evaluate":[76],"complex":[78,102,117,123,215],"models":[79,179,209],"provide":[81],"significant":[82],"utility":[83],"this":[85],"emerging":[86],"area":[87],"research.":[92],"RESULTS:":[93],"We":[94],"propose":[95],"a":[96,120,144,220],"novel":[97],"graph":[98],"transformer-based":[99],"approach":[100],"named":[101],"RNA":[106],"(CARP)":[109],"infer":[111],"multiple":[112,131],"perspectives":[114],"models.":[118,236],"For":[119],"single":[121],"model,":[124],"one":[126],"shot,":[127],"CARP":[128,174,217,240],"simultaneously":[129],"predicts":[130],"overall":[132,134],"fold,":[133],"interface,":[135],"per-protein-RNA":[137],"interface":[138,192,196],"estimates.":[140],"When":[141],"evaluated":[142],"against":[143],"non-redundant":[145],"docking":[147],"benchmark,":[148],"our":[149],"demonstrated":[151],"obvious":[152],"improved":[153],"performance":[154],"compared":[155,223],"almost":[157],"all":[158,211],"existing":[161,226],"scoring":[162],"tools,":[163],"particularly":[164],"when":[165,184],"ordering":[166],"selecting":[168,232],"highest":[170],"decoys.":[172],"Furthermore,":[173],"consistently":[175],"selected":[176,207],"higher":[177],"relative":[180],"other":[182],"predictors":[183],"tested":[185],"on":[186,205],"CASP16":[187,213],"targets.":[188,216],"Specifically,":[189],"CARP-predicted":[190],"global":[191,194],"qualities":[197],"were":[198],"ranked":[199],"first":[200],"second,":[202],"respectively,":[203],"based":[204],"top-3":[208],"over":[210],"ten":[212],"also":[218],"showed":[219],"strong":[221],"ability,":[222],"both":[225],"tools":[227],"AlphaFold3":[229,235],"self-estimates,":[230],"high":[233],"AVAILABILITY":[237],"AND":[238],"IMPLEMENTATION:":[239],"freely":[242],"available":[243],"at":[244],"github.com/zwang-bioinformatics/CARP/.":[245]},"counts_by_year":[],"updated_date":"2026-06-27T08:28:00.272161","created_date":"2026-04-30T00:00:00"}