{"id":"https://openalex.org/W2951690294","doi":"https://doi.org/10.1093/bioinformatics/btz122","title":"Protein model quality assessment using 3D oriented convolutional neural networks","display_name":"Protein model quality assessment using 3D oriented convolutional neural networks","publication_year":2019,"publication_date":"2019-02-17","ids":{"openalex":"https://openalex.org/W2951690294","doi":"https://doi.org/10.1093/bioinformatics/btz122","mag":"2951690294","pmid":"https://pubmed.ncbi.nlm.nih.gov/30874723"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz122","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz122","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"green","oa_url":"https://inria.hal.science/hal-01899468","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004359429","display_name":"Guillaume Pag\u00e8s","orcid":null},"institutions":[{"id":"https://openalex.org/I106785703","display_name":"Institut polytechnique de Grenoble","ror":"https://ror.org/05sbt2524","country_code":"FR","type":"education","lineage":["https://openalex.org/I106785703","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I4210149092","display_name":"Laboratoire Jean Kuntzmann","ror":"https://ror.org/04ett5b41","country_code":"FR","type":"facility","lineage":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210149092","https://openalex.org/I899635006","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Guillaume Pag\u00e8s","raw_affiliation_strings":["Universit\u00e9 Grenoble Alpes, Inria, CNRS , Grenoble INP, LJK, Grenoble, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Grenoble Alpes, Inria, CNRS , Grenoble INP, LJK, Grenoble, France","institution_ids":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I4210101348","https://openalex.org/I4210149092","https://openalex.org/I899635006"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089253014","display_name":"Benoit Charmettant","orcid":null},"institutions":[{"id":"https://openalex.org/I106785703","display_name":"Institut polytechnique de Grenoble","ror":"https://ror.org/05sbt2524","country_code":"FR","type":"education","lineage":["https://openalex.org/I106785703","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I4210149092","display_name":"Laboratoire Jean Kuntzmann","ror":"https://ror.org/04ett5b41","country_code":"FR","type":"facility","lineage":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210149092","https://openalex.org/I899635006","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Benoit Charmettant","raw_affiliation_strings":["Universit\u00e9 Grenoble Alpes, Inria, CNRS , Grenoble INP, LJK, Grenoble, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Grenoble Alpes, Inria, CNRS , Grenoble INP, LJK, Grenoble, France","institution_ids":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I4210101348","https://openalex.org/I4210149092","https://openalex.org/I899635006"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009307435","display_name":"Sergei Grudinin","orcid":"https://orcid.org/0000-0002-1903-7220"},"institutions":[{"id":"https://openalex.org/I106785703","display_name":"Institut polytechnique de Grenoble","ror":"https://ror.org/05sbt2524","country_code":"FR","type":"education","lineage":["https://openalex.org/I106785703","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I4210101348","display_name":"Centre Inria de l'Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/00n8d6z93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1326498283","https://openalex.org/I4210101348"]},{"id":"https://openalex.org/I4210149092","display_name":"Laboratoire Jean Kuntzmann","ror":"https://ror.org/04ett5b41","country_code":"FR","type":"facility","lineage":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I4210149092","https://openalex.org/I899635006","https://openalex.org/I899635006"]},{"id":"https://openalex.org/I899635006","display_name":"Universit\u00e9 Grenoble Alpes","ror":"https://ror.org/02rx3b187","country_code":"FR","type":"education","lineage":["https://openalex.org/I899635006"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Sergei Grudinin","raw_affiliation_strings":["Universit\u00e9 Grenoble Alpes, Inria, CNRS , Grenoble INP, LJK, Grenoble, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Grenoble Alpes, Inria, CNRS , Grenoble INP, LJK, Grenoble, France","institution_ids":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I4210101348","https://openalex.org/I4210149092","https://openalex.org/I899635006"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5009307435"],"corresponding_institution_ids":["https://openalex.org/I106785703","https://openalex.org/I1294671590","https://openalex.org/I4210101348","https://openalex.org/I4210149092","https://openalex.org/I899635006"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":5.0867,"has_fulltext":false,"cited_by_count":108,"citation_normalized_percentile":{"value":0.96658604,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"35","issue":"18","first_page":"3313","last_page":"3319"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.777400016784668,"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":0.777400016784668,"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/T11162","display_name":"Enzyme Structure and Function","score":0.10790000110864639,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.03840000182390213,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.8380303382873535},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7542502880096436},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4776631295681},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.46573391556739807},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.45479729771614075},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4011518359184265}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.8380303382873535},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7542502880096436},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4776631295681},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46573391556739807},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.45479729771614075},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4011518359184265},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz122","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz122","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30874723","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30874723","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:HAL:hal-01899468v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-01899468","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"Bioinformatics, 2019, 35 (18), pp.3313-3319. &#x27E8;10.1093/bioinformatics/btz122&#x27E9;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-01899468v1","is_oa":true,"landing_page_url":"https://inria.hal.science/hal-01899468","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"Bioinformatics, 2019, 35 (18), pp.3313-3319. &#x27E8;10.1093/bioinformatics/btz122&#x27E9;","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G123004181","display_name":null,"funder_award_id":"ANR\u201015\u2010CE11\u20100029\u201003","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G325687231","display_name":"New light-driven channels and transporters for optogenetics","funder_award_id":"ANR-15-CE11-0029","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1836465849","https://openalex.org/W2025183033","https://openalex.org/W2048290645","https://openalex.org/W2062123114","https://openalex.org/W2071486470","https://openalex.org/W2076048958","https://openalex.org/W2106154817","https://openalex.org/W2109383908","https://openalex.org/W2113267464","https://openalex.org/W2117451312","https://openalex.org/W2123085274","https://openalex.org/W2130325614","https://openalex.org/W2140673705","https://openalex.org/W2141783940","https://openalex.org/W2161151688","https://openalex.org/W2176412452","https://openalex.org/W2201713963","https://openalex.org/W2214665483","https://openalex.org/W2290283816","https://openalex.org/W2402144811","https://openalex.org/W2418704427","https://openalex.org/W2514534732","https://openalex.org/W2534288757","https://openalex.org/W2576915720","https://openalex.org/W2583907533","https://openalex.org/W2594725344","https://openalex.org/W2617750324","https://openalex.org/W2784883284","https://openalex.org/W2810448195","https://openalex.org/W2889674656","https://openalex.org/W2905812122","https://openalex.org/W2912918068","https://openalex.org/W2963285578","https://openalex.org/W3104705366","https://openalex.org/W3198971594","https://openalex.org/W4394650427","https://openalex.org/W6638667902","https://openalex.org/W6685562342","https://openalex.org/W6688357764","https://openalex.org/W6696356757","https://openalex.org/W6713134421","https://openalex.org/W6728530719","https://openalex.org/W6731845922","https://openalex.org/W6752552213"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein":[1],"model":[2,44,94,133,243],"quality":[3,134],"assessment":[4],"(QA)":[5],"is":[6,45,113,212],"a":[7,48,85,114,136,219,231],"crucial":[8],"and":[9,130,151,180,193,230],"yet":[10],"open":[11],"problem":[12,91,164],"in":[13,38,186],"structural":[14],"bioinformatics.":[15],"The":[16,210],"current":[17],"best":[18],"methods":[19],"for":[20,109,239],"single-model":[21,110,204],"QA":[22,205],"typically":[23],"combine":[24],"results":[25],"from":[26],"different":[27,32],"approaches,":[28],"each":[29,149],"based":[30,234],"on":[31,235],"input":[33,121,144],"features":[34,70],"constructed":[35],"by":[36,75],"experts":[37],"the":[39,42,53,60,68,90,127,131,143,155,163,169,184,187,197,236,241],"field.":[40],"Then,":[41],"prediction":[43],"trained":[46,77],"using":[47],"machine-learning":[49],"algorithm.":[50],"Recently,":[51],"with":[52,104,154],"development":[54],"of":[55,92,158,165,168,177,183,200,218],"convolutional":[56,78],"neural":[57],"networks":[58],"(CNN),":[59],"training":[61],"paradigm":[62],"has":[63],"changed.":[64],"In":[65],"computer":[66],"vision,":[67],"expert-developed":[69],"have":[71],"been":[72],"significantly":[73],"overpassed":[74],"automatically":[76],"filters.":[79],"This":[80,161],"motivated":[81],"us":[82],"to":[83,89,148,244],"apply":[84],"three-dimensional":[86],"(3D)":[87],"CNN":[88],"protein":[93],"QA.":[95,111],"RESULTS:":[96],"We":[97],"developed":[98],"Ornate":[99,112,141,173,242],"(Oriented":[100],"Routed":[101],"Neural":[102],"network":[103],"Automatic":[105],"Typing)-a":[106],"novel":[107],"method":[108,211],"residue-wise":[115],"scoring":[116],"function":[117],"that":[118,222],"takes":[119],"as":[120],"3D":[122,138],"density":[123,145,228],"maps.":[124,246],"It":[125,216],"predicts":[126],"local":[128],"(residue-wise)":[129],"global":[132],"through":[135],"deep":[137],"CNN.":[139],"Specifically,":[140],"aligns":[142],"map,":[146],"corresponding":[147],"residue":[150],"its":[152],"neighborhood,":[153],"backbone":[156],"topology":[157],"this":[159],"residue.":[160],"circumvents":[162],"ambiguous":[166],"orientations":[167],"initial":[170],"models.":[171],"Also,":[172],"includes":[174],"automatic":[175],"identification":[176],"atom":[178],"types":[179],"dynamic":[181],"routing":[182],"data":[185,250],"network.":[188],"Established":[189],"benchmarks":[190],"(CASP":[191],"11":[192],"CASP":[194],"12)":[195],"demonstrate":[196],"state-of-the-art":[198],"performance":[199],"our":[201],"approach":[202],"among":[203],"methods.":[206],"AVAILABILITY":[207],"AND":[208],"IMPLEMENTATION:":[209],"available":[213,252],"at":[214,253],"https://team.inria.fr/nano-d/software/Ornate/.":[215],"consists":[217],"C++":[220],"executable":[221],"transforms":[223],"molecular":[224],"structures":[225],"into":[226],"volumetric":[227],"maps,":[229],"Python":[232],"code":[233],"TensorFlow":[237],"framework":[238],"applying":[240],"these":[245],"SUPPLEMENTARY":[247],"INFORMATION:":[248],"Supplementary":[249],"are":[251],"Bioinformatics":[254],"online.":[255]},"counts_by_year":[{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":22},{"year":2021,"cited_by_count":23},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":6}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
