{"id":"https://openalex.org/W4409656140","doi":"https://doi.org/10.1021/acs.jcim.5c00176","title":"SeqMG-RPI: A Sequence-Based Framework Integrating Multi-Scale RNA Features and Protein Graphs for RNA-Protein Interaction Prediction","display_name":"SeqMG-RPI: A Sequence-Based Framework Integrating Multi-Scale RNA Features and Protein Graphs for RNA-Protein Interaction Prediction","publication_year":2025,"publication_date":"2025-04-22","ids":{"openalex":"https://openalex.org/W4409656140","doi":"https://doi.org/10.1021/acs.jcim.5c00176","pmid":"https://pubmed.ncbi.nlm.nih.gov/40262169"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00176","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00176","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019843586","display_name":"Teng Ma","orcid":"https://orcid.org/0009-0005-5355-5231"},"institutions":[{"id":"https://openalex.org/I44468530","display_name":"Qingdao University of Technology","ror":"https://ror.org/01qzc0f54","country_code":"CN","type":"education","lineage":["https://openalex.org/I44468530"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Teng Ma","raw_affiliation_strings":["Qingdao University of Technology","School of Information and Control Engineering"],"raw_orcid":"https://orcid.org/0009-0005-5355-5231","affiliations":[{"raw_affiliation_string":"Qingdao University of Technology","institution_ids":["https://openalex.org/I44468530"]},{"raw_affiliation_string":"School of Information and Control Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076937227","display_name":"Mingjian Jiang","orcid":"https://orcid.org/0000-0002-0716-5292"},"institutions":[{"id":"https://openalex.org/I44468530","display_name":"Qingdao University of Technology","ror":"https://ror.org/01qzc0f54","country_code":"CN","type":"education","lineage":["https://openalex.org/I44468530"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Mingjian Jiang","raw_affiliation_strings":["Qingdao University of Technology","School of Information and Control Engineering"],"raw_orcid":"https://orcid.org/0000-0002-0716-5292","affiliations":[{"raw_affiliation_string":"Qingdao University of Technology","institution_ids":["https://openalex.org/I44468530"]},{"raw_affiliation_string":"School of Information and Control Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056260594","display_name":"Shunpeng Pang","orcid":null},"institutions":[{"id":"https://openalex.org/I66883779","display_name":"Weifang University","ror":"https://ror.org/01frp7483","country_code":"CN","type":"education","lineage":["https://openalex.org/I66883779"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shunpeng Pang","raw_affiliation_strings":["School of Computer Engineering","Weifang University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Engineering","institution_ids":[]},{"raw_affiliation_string":"Weifang University","institution_ids":["https://openalex.org/I66883779"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100410681","display_name":"Zhi Zhang","orcid":"https://orcid.org/0000-0001-9002-0360"},"institutions":[{"id":"https://openalex.org/I44468530","display_name":"Qingdao University of Technology","ror":"https://ror.org/01qzc0f54","country_code":"CN","type":"education","lineage":["https://openalex.org/I44468530"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhi Zhang","raw_affiliation_strings":["Qingdao University of Technology","School of Information and Control Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Qingdao University of Technology","institution_ids":["https://openalex.org/I44468530"]},{"raw_affiliation_string":"School of Information and Control Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Huaibin Hang","orcid":null},"institutions":[{"id":"https://openalex.org/I44468530","display_name":"Qingdao University of Technology","ror":"https://ror.org/01qzc0f54","country_code":"CN","type":"education","lineage":["https://openalex.org/I44468530"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huaibin Hang","raw_affiliation_strings":["Qingdao University of Technology","School of Information and Control Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Qingdao University of Technology","institution_ids":["https://openalex.org/I44468530"]},{"raw_affiliation_string":"School of Information and Control Engineering","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005510423","display_name":"Wei Zhou","orcid":"https://orcid.org/0000-0001-5956-0684"},"institutions":[{"id":"https://openalex.org/I44468530","display_name":"Qingdao University of Technology","ror":"https://ror.org/01qzc0f54","country_code":"CN","type":"education","lineage":["https://openalex.org/I44468530"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Zhou","raw_affiliation_strings":["Qingdao University of Technology","School of Information and Control Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Qingdao University of Technology","institution_ids":["https://openalex.org/I44468530"]},{"raw_affiliation_string":"School of Information and Control Engineering","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100746477","display_name":"Yuanyuan Zhang","orcid":"https://orcid.org/0000-0003-3935-3201"},"institutions":[{"id":"https://openalex.org/I44468530","display_name":"Qingdao University of Technology","ror":"https://ror.org/01qzc0f54","country_code":"CN","type":"education","lineage":["https://openalex.org/I44468530"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanyuan Zhang","raw_affiliation_strings":["Qingdao University of Technology","School of Information and Control Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Qingdao University of Technology","institution_ids":["https://openalex.org/I44468530"]},{"raw_affiliation_string":"School of Information and Control Engineering","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5076937227"],"corresponding_institution_ids":["https://openalex.org/I44468530"],"apc_list":null,"apc_paid":null,"fwci":1.4604,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.80507266,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"65","issue":"9","first_page":"4698","last_page":"4713"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9991999864578247,"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/T11482","display_name":"RNA modifications and cancer","score":0.9980999827384949,"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/rna","display_name":"RNA","score":0.6181644797325134},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.569432258605957},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5104478597640991},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47636768221855164},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.449725866317749},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.41469213366508484},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28241610527038574},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.18252980709075928},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1443522572517395},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08545097708702087}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6181644797325134},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.569432258605957},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5104478597640991},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47636768221855164},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.449725866317749},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.41469213366508484},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28241610527038574},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.18252980709075928},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1443522572517395},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08545097708702087},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c00176","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00176","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40262169","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40262169","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2122243128","display_name":null,"funder_award_id":"No. WFU2023BS47","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"}],"funders":[{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W2025150647","https://openalex.org/W2064515831","https://openalex.org/W2072394638","https://openalex.org/W2119501676","https://openalex.org/W2130479394","https://openalex.org/W2315196278","https://openalex.org/W2336850185","https://openalex.org/W2507804718","https://openalex.org/W2896541477","https://openalex.org/W2901968680","https://openalex.org/W2914842084","https://openalex.org/W2920083709","https://openalex.org/W2920229364","https://openalex.org/W2971428843","https://openalex.org/W2989219518","https://openalex.org/W3002341417","https://openalex.org/W3021002099","https://openalex.org/W3032123378","https://openalex.org/W3112802026","https://openalex.org/W3125850677","https://openalex.org/W3130271948","https://openalex.org/W3135611359","https://openalex.org/W3170959707","https://openalex.org/W4214812055","https://openalex.org/W4220660070","https://openalex.org/W4220898336","https://openalex.org/W4297733535","https://openalex.org/W4311390313","https://openalex.org/W4313644806","https://openalex.org/W4319444998","https://openalex.org/W4323842603","https://openalex.org/W4375954779","https://openalex.org/W4377094475","https://openalex.org/W4378084633","https://openalex.org/W4394984695","https://openalex.org/W4396821501","https://openalex.org/W4398202116","https://openalex.org/W4400802404","https://openalex.org/W4403394241","https://openalex.org/W4403654499","https://openalex.org/W4404171434"],"related_works":["https://openalex.org/W2147993839","https://openalex.org/W2099982459","https://openalex.org/W2109298101","https://openalex.org/W2007507741","https://openalex.org/W2159860826","https://openalex.org/W3192210502","https://openalex.org/W1981737222","https://openalex.org/W1569394480","https://openalex.org/W4390876228","https://openalex.org/W1998222399"],"abstract_inverted_index":{"RNA-protein":[0],"interaction":[1],"(RPI)":[2],"plays":[3],"a":[4,33,48,70,74,80,90,99],"crucial":[5],"role":[6],"in":[7],"cell":[8],"biology,":[9],"and":[10,21,36,79,109,134],"accurate":[11],"prediction":[12,28,52],"of":[13],"RPI":[14,27,51,110],"is":[15,38,104,121],"essential":[16],"to":[17,94],"understand":[18],"molecular":[19],"mechanisms":[20],"advance":[22],"disease":[23],"research.":[24],"Some":[25],"existing":[26,128],"methods":[29],"typically":[30],"rely":[31],"on":[32],"single":[34],"feature":[35,64,93,107],"there":[37],"significant":[39],"room":[40],"for":[41,106],"improvement.":[42],"In":[43],"this":[44],"paper,":[45],"we":[46],"propose":[47],"novel":[49,100],"sequence-based":[50,68],"method,":[53],"called":[54],"SeqMG-RPI.":[55],"For":[56,86],"RNA,":[57],"SeqMG-RPI":[58,88],"introduces":[59],"an":[60],"innovative":[61],"multi-scale":[62],"RNA":[63,72],"that":[65,123],"integrates":[66],"three":[67],"representations:":[69],"multi-channel":[71],"feature,":[73,78],"k":[75,81],"-mer":[76,82],"frequency":[77],"sparse":[83],"matrix":[84],"feature.":[85],"protein,":[87],"utilizes":[89],"graph-based":[91],"protein":[92,96],"capture":[95],"information.":[97],"Moreover,":[98],"neural":[101],"network":[102],"architecture":[103],"constructed":[105],"extraction":[108],"prediction.":[111],"Through":[112],"experiments":[113],"from":[114],"multiple":[115],"perspectives":[116],"across":[117],"various":[118],"datasets,":[119],"it":[120],"demonstrated":[122],"the":[124],"proposed":[125],"method":[126],"outperforms":[127],"methods,":[129],"which":[130],"has":[131],"better":[132],"performance":[133],"generalization.":[135]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-14T06:11:07.267592","created_date":"2025-10-10T00:00:00"}
