{"id":"https://openalex.org/W4390619601","doi":"https://doi.org/10.1093/bioadv/vbad191","title":"DeepRank-GNN-esm: a graph neural network for scoring protein\u2013protein models using protein language model","display_name":"DeepRank-GNN-esm: a graph neural network for scoring protein\u2013protein models using protein language model","publication_year":2023,"publication_date":"2023-12-29","ids":{"openalex":"https://openalex.org/W4390619601","doi":"https://doi.org/10.1093/bioadv/vbad191","pmid":"https://pubmed.ncbi.nlm.nih.gov/38213822","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/10782804"},"language":"en","primary_location":{"id":"doi:10.1093/bioadv/vbad191","doi":"https://doi.org/10.1093/bioadv/vbad191","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioadv/vbad191","pdf_url":"https://academic.oup.com/bioinformaticsadvances/advance-article-pdf/doi/10.1093/bioadv/vbad191/55117264/vbad191.pdf","source":{"id":"https://openalex.org/S4210234069","display_name":"Bioinformatics Advances","issn_l":"2635-0041","issn":["2635-0041"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1","oarl"],"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 Advances","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://academic.oup.com/bioinformaticsadvances/advance-article-pdf/doi/10.1093/bioadv/vbad191/55117264/vbad191.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101454232","display_name":"Xiaotong Xu","orcid":"https://orcid.org/0009-0006-1883-6692","observed_orcids":["https://orcid.org/0009-0006-1883-6692"]},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Xiaotong Xu","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research , Utrecht 3584 CS, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research , Utrecht 3584 CS, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064072429","display_name":"Alexandre M. J. J. Bonvin","orcid":"https://orcid.org/0000-0001-7369-1322","observed_orcids":["https://orcid.org/0000-0001-7369-1322"]},"institutions":[{"id":"https://openalex.org/I193662353","display_name":"Utrecht University","ror":"https://ror.org/04pp8hn57","country_code":"NL","type":"education","lineage":["https://openalex.org/I193662353"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Alexandre M J J Bonvin","raw_affiliation_strings":["Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research , Utrecht 3584 CS, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0001-7369-1322","affiliations":[{"raw_affiliation_string":"Department of Chemistry, Faculty of Science, Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research , Utrecht 3584 CS, The Netherlands","institution_ids":["https://openalex.org/I193662353"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5064072429"],"corresponding_institution_ids":["https://openalex.org/I193662353"],"apc_list":{"value":2472,"currency":"USD","value_usd":2472},"apc_paid":{"value":2472,"currency":"USD","value_usd":2472},"fwci":3.1667,"has_fulltext":true,"cited_by_count":41,"citation_normalized_percentile":{"value":0.94253985,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"4","issue":"1","first_page":"vbad191","last_page":"vbad191"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.8179000020027161,"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":0.8179000020027161,"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":0.0723000019788742,"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":0.06319999694824219,"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-interaction","display_name":"protein-protein interaction","score":0.9190000295639038},{"id":"https://openalex.org/keywords/graph-neural-networks","display_name":"graph neural networks","score":0.8009999990463257},{"id":"https://openalex.org/keywords/esm-2-embeddings","display_name":"ESM-2 embeddings","score":0.7979999780654907},{"id":"https://openalex.org/keywords/protein-language-models","display_name":"protein language models","score":0.9309999942779541},{"id":"https://openalex.org/keywords/position-specific-scoring-matrix","display_name":"position weight matrices","score":0.8489999771118164}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5912148952484131},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5230886936187744},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4376784563064575},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39737510681152344},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.34626883268356323},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.08529889583587646}],"mesh":[],"locations_count":7,"locations":[{"id":"doi:10.1093/bioadv/vbad191","doi":"https://doi.org/10.1093/bioadv/vbad191","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioadv/vbad191","pdf_url":"https://academic.oup.com/bioinformaticsadvances/advance-article-pdf/doi/10.1093/bioadv/vbad191/55117264/vbad191.pdf","source":{"id":"https://openalex.org/S4210234069","display_name":"Bioinformatics Advances","issn_l":"2635-0041","issn":["2635-0041"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1","oarl"],"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 Advances","raw_type":"journal-article"},{"id":"doi:10.1101/2023.06.22.546080","doi":"https://doi.org/10.1101/2023.06.22.546080","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2023.06.22.546080","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2023/06/24/2023.06.22.546080.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"},{"id":"pmh:oai:pubmedcentral.nih.gov:10782804","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10782804","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10782804/pdf/vbad191.pdf","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":"Bioinform Adv","raw_type":"Text"},{"id":"pmid:38213822","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38213822","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 advances","raw_type":"Journal Article"},{"id":"pmh:oai:dspace.library.uu.nl:1874/436014","doi":null,"is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/436014","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"/dk/atira/pure/researchoutput/researchoutputtypes/workingpaper/preprint"},{"id":"pmh:oai:dspace.library.uu.nl:1874/437608","doi":null,"is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/437608","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:dspace.library.uu.nl:1874/438082","doi":null,"is_oa":true,"landing_page_url":"https://dspace.library.uu.nl/handle/1874/438082","pdf_url":null,"source":{"id":"https://openalex.org/S4306401649","display_name":"Utrecht University Repository (Utrecht University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I193662353","host_organization_name":"Utrecht University","host_organization_lineage":["https://openalex.org/I193662353"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioadv/vbad191","doi":"https://doi.org/10.1093/bioadv/vbad191","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioadv/vbad191","pdf_url":"https://academic.oup.com/bioinformaticsadvances/advance-article-pdf/doi/10.1093/bioadv/vbad191/55117264/vbad191.pdf","source":{"id":"https://openalex.org/S4210234069","display_name":"Bioinformatics Advances","issn_l":"2635-0041","issn":["2635-0041"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-1","oarl"],"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 Advances","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3471917844","display_name":"BioExcel Centre of Excellence for ComputationalBiomolecular Research","funder_award_id":"823830","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G434337789","display_name":null,"funder_award_id":"HORIZON2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5155615645","display_name":null,"funder_award_id":"202208310024","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390619601.pdf","grobid_xml":"https://content.openalex.org/works/W4390619601.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1030883578","https://openalex.org/W1907442748","https://openalex.org/W2081598613","https://openalex.org/W2099712765","https://openalex.org/W2140574901","https://openalex.org/W2153983456","https://openalex.org/W2162259397","https://openalex.org/W2292767755","https://openalex.org/W2774836764","https://openalex.org/W2909255640","https://openalex.org/W2950365860","https://openalex.org/W2990689232","https://openalex.org/W2991012415","https://openalex.org/W2991359755","https://openalex.org/W3137835966","https://openalex.org/W3164107346","https://openalex.org/W3177828909","https://openalex.org/W3202105508","https://openalex.org/W3216616254","https://openalex.org/W4206075523","https://openalex.org/W4206900467","https://openalex.org/W4220887281","https://openalex.org/W4220933909","https://openalex.org/W4220990251","https://openalex.org/W4297235560","https://openalex.org/W4309862248","https://openalex.org/W4312065672","https://openalex.org/W4312106927","https://openalex.org/W4313826102","https://openalex.org/W4327550249","https://openalex.org/W4382181821","https://openalex.org/W4383216409","https://openalex.org/W6601365666","https://openalex.org/W6602430550","https://openalex.org/W6746305829"],"related_works":["https://openalex.org/W6929420548","https://openalex.org/W4309862248","https://openalex.org/W4402458171","https://openalex.org/W4405910786","https://openalex.org/W4416347461","https://openalex.org/W4380625376","https://openalex.org/W3216616254","https://openalex.org/W4319050297","https://openalex.org/W4393620727","https://openalex.org/W4400104779"],"abstract_inverted_index":{"Motivation:":[0],"Protein-Protein":[1],"interactions":[2],"(PPIs)":[3],"play":[4],"critical":[5],"roles":[6],"in":[7,37],"numerous":[8],"cellular":[9],"processes.":[10],"By":[11],"modelling":[12,39],"the":[13,17,38,43,49,87,101,119,125,131,159,166,169],"3D":[14],"structures":[15],"of":[16,45,52,161,168],"correspond":[18],"protein":[19,33,114],"complexes":[20],"valuable":[21],"insights":[22],"can":[23,128],"be":[24,183],"obtained,":[25],"providing,":[26],"e.g.":[27],"starting":[28],"points":[29],"for":[30,176,178],"drug":[31],"and":[32,70,149,171,192],"design.":[34],"One":[35],"challenge":[36],"process":[40],"is":[41,195],"however":[42],"identification":[44],"near-native":[46],"models":[47],"from":[48,118,198],"large":[50],"pool":[51],"generated":[53],"models.":[54],"To":[55],"this":[56],"end":[57],"we":[58],"have":[59],"previously":[60],"developed":[61],"DeepRank-GNN,":[62],"a":[63],"graph":[64],"neural":[65],"network":[66],"that":[67,109,124],"integrates":[68],"structural":[69],"sequence":[71],"information":[72],"to":[73,86,97],"enable":[74],"effective":[75],"pattern":[76],"learning":[77],"at":[78,134],"PPI":[79],"interfaces.":[80],"Its":[81],"main":[82],"features":[83,113,133],"are":[84,94,186],"related":[85],"Position":[88],"Specific":[89],"Scoring":[90],"Matrices":[91],"(PSSMs),":[92],"which":[93,179],"computationally":[95],"expensive":[96],"generate,":[98],"significantly":[99],"limits":[100],"algorithm's":[102],"usability.":[103],"Results:":[104],"We":[105,122],"introduce":[106],"here":[107],"DeepRank-GNN-esm":[108,194],"includes":[110],"as":[111],"additional":[112],"language":[115],"model":[116],"embeddings":[117,127],"ESM-2":[120,126],"model.":[121],"show":[123],"actually":[129],"replace":[130],"PSSM":[132,180],"no":[135],"cost":[136],"in-,":[137],"or":[138,185],"even":[139],"better":[140],"performance":[141],"on":[142],"two":[143],"PPI-related":[144],"tasks:":[145],"scoring":[146],"docking":[147],"poses":[148],"detecting":[150],"crystal":[151],"artifacts.":[152],"This":[153],"new":[154,173],"DeepRank":[155],"version":[156],"bypasses":[157],"thus":[158],"need":[160],"generating":[162],"PSSM,":[163],"greatly":[164],"improving":[165],"usability":[167],"software":[170],"opening":[172],"application":[174],"opportunities":[175],"systems":[177],"profiles":[181],"cannot":[182],"obtained":[184],"irrelevant":[187],"(e.g.":[188],"antibody-antigen":[189],"complexes).":[190],"Availability":[191],"implementation:":[193],"freely":[196],"available":[197],"https://github.com/DeepRank/DeepRank-GNN-esm.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":19},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":7}],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2024-01-07T00:00:00"}
