{"id":"https://openalex.org/W2950428375","doi":"https://doi.org/10.48550/arxiv.1607.04379","title":"DeepQA: Improving the estimation of single protein model quality with deep belief networks","display_name":"DeepQA: Improving the estimation of single protein model quality with deep belief networks","publication_year":2016,"publication_date":"2016-07-15","ids":{"openalex":"https://openalex.org/W2950428375","doi":"https://doi.org/10.48550/arxiv.1607.04379","mag":"2950428375"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:1607.04379","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1607.04379","pdf_url":"https://arxiv.org/pdf/1607.04379","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"volume":null,"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1607.04379","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085487073","display_name":"Renzhi Cao","orcid":"https://orcid.org/0000-0002-8345-343X","observed_orcids":["https://orcid.org/0000-0002-8345-343X"]},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cao, Renzhi","raw_affiliation_strings":["Department of Computer Science , University of Missouri , Columbia , MO 65211 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science , University of Missouri , Columbia , MO 65211 , USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018409409","display_name":"Debswapna Bhattacharya","orcid":"https://orcid.org/0000-0002-9630-0141","observed_orcids":["https://orcid.org/0000-0002-9630-0141"]},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bhattacharya, Debswapna","raw_affiliation_strings":["Department of Computer Science , University of Missouri , Columbia , MO 65211 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science , University of Missouri , Columbia , MO 65211 , USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022495891","display_name":"Jie Hou","orcid":"https://orcid.org/0000-0002-8584-5154","observed_orcids":["https://orcid.org/0000-0002-8584-5154","https://orcid.org/0009-0003-2250-0532"]},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hou, Jie","raw_affiliation_strings":["Department of Computer Science , University of Missouri , Columbia , MO 65211 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science , University of Missouri , Columbia , MO 65211 , USA","institution_ids":["https://openalex.org/I76835614"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044354277","display_name":"Jianlin Jack Cheng","orcid":"https://orcid.org/0000-0003-0305-2853","observed_orcids":["https://orcid.org/0000-0003-0305-2853"]},"institutions":[{"id":"https://openalex.org/I76835614","display_name":"University of Missouri","ror":"https://ror.org/02ymw8z06","country_code":"US","type":"education","lineage":["https://openalex.org/I76835614"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cheng, Jianlin","raw_affiliation_strings":["Department of Computer Science , University of Missouri , Columbia , MO 65211 , USA","Informatics Institute , University of Missouri , Columbia , Missouri , 65211 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science , University of Missouri , Columbia , MO 65211 , USA","institution_ids":["https://openalex.org/I76835614"]},{"raw_affiliation_string":"Informatics Institute , University of Missouri , Columbia , Missouri , 65211 , USA","institution_ids":["https://openalex.org/I76835614"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I76835614"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":4,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9907000064849854,"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":0.9907000064849854,"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":0.004699999932199717,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.00139999995008111,"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/deep-belief-network","display_name":"deep belief network","score":0.9390000104904175},{"id":"https://openalex.org/keywords/protein-tertiary-structure-prediction","display_name":"protein tertiary structure prediction","score":0.8799999952316284},{"id":"https://openalex.org/keywords/model-ranking","display_name":"model ranking","score":0.4740000069141388},{"id":"https://openalex.org/keywords/caspase-11","display_name":"caspase-11","score":0.7419999837875366},{"id":"https://openalex.org/keywords/energy-characteristics","display_name":"energy characteristics","score":0.4830000102519989},{"id":"https://openalex.org/keywords/physicochemical-properties","display_name":"physicochemical properties","score":0.8349999785423279},{"id":"https://openalex.org/keywords/structural-features","display_name":"structural features","score":0.9089999794960022}],"concepts":[{"id":"https://openalex.org/C66153294","wikidata":"https://www.wikidata.org/wiki/Q899291","display_name":"CASP","level":4,"score":0.770439624786377},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7694908380508423},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.717831015586853},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6116182804107666},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5916552543640137},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5911240577697754},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.574537456035614},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.5671361088752747},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5500355362892151},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.5412539839744568},{"id":"https://openalex.org/C119898033","wikidata":"https://www.wikidata.org/wiki/Q3433888","display_name":"Ensemble forecasting","level":2,"score":0.42899060249328613},{"id":"https://openalex.org/C79337645","wikidata":"https://www.wikidata.org/wiki/Q779824","display_name":"Outlier","level":2,"score":0.42768311500549316},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.1569419503211975},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"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},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:1607.04379","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1607.04379","pdf_url":"https://arxiv.org/pdf/1607.04379","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.1607.04379","doi":"https://doi.org/10.48550/arxiv.1607.04379","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1607.04379","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1607.04379","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1607.04379","pdf_url":"https://arxiv.org/pdf/1607.04379","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G7450496187","display_name":"Distance-based ab initio protein structure prediction","funder_award_id":"R01GM093123","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"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":46,"referenced_works":["https://openalex.org/W95630632","https://openalex.org/W273955616","https://openalex.org/W1663797894","https://openalex.org/W1965615878","https://openalex.org/W2008505479","https://openalex.org/W2008708467","https://openalex.org/W2016707108","https://openalex.org/W2031721366","https://openalex.org/W2033357321","https://openalex.org/W2043304335","https://openalex.org/W2047221353","https://openalex.org/W2057899197","https://openalex.org/W2066507577","https://openalex.org/W2071486470","https://openalex.org/W2093567555","https://openalex.org/W2096495474","https://openalex.org/W2108376320","https://openalex.org/W2116064496","https://openalex.org/W2116672918","https://openalex.org/W2117451312","https://openalex.org/W2119908016","https://openalex.org/W2123085274","https://openalex.org/W2125165264","https://openalex.org/W2140454691","https://openalex.org/W2140574901","https://openalex.org/W2145991251","https://openalex.org/W2150297520","https://openalex.org/W2150831049","https://openalex.org/W2152811165","https://openalex.org/W2153153865","https://openalex.org/W2154106236","https://openalex.org/W2155201844","https://openalex.org/W2159614853","https://openalex.org/W2160784118","https://openalex.org/W2161151688","https://openalex.org/W2167661287","https://openalex.org/W2167719367","https://openalex.org/W2172637956","https://openalex.org/W2173669824","https://openalex.org/W2257979135","https://openalex.org/W2262829055","https://openalex.org/W2290412022","https://openalex.org/W2411608355","https://openalex.org/W2411622282","https://openalex.org/W2418704427","https://openalex.org/W2419006500"],"related_works":["https://openalex.org/W3113027540","https://openalex.org/W3004583155","https://openalex.org/W2417306259","https://openalex.org/W2807524936","https://openalex.org/W2805338223","https://openalex.org/W6939994244","https://openalex.org/W3109027947","https://openalex.org/W7002458442","https://openalex.org/W2950101111","https://openalex.org/W2796925135"],"abstract_inverted_index":{"Protein":[0,116],"quality":[1,28,65,83,156,190,206],"assessment":[2,66,157,207],"(QA)":[3],"by":[4,128,192],"ranking":[5],"and":[6,95,125,149,159,208,217],"selecting":[7,38,177],"protein":[8,21,32,154,203,209],"models":[9,42,110,126,180,186],"has":[10,141],"long":[11],"been":[12],"viewed":[13],"as":[14,91],"one":[15],"of":[16,29,44,50,78,84,109,115,185,187,220],"the":[17,27,82,112,153,164],"major":[18],"challenges":[19],"for":[20,37,202,222],"tertiary":[22],"structure":[23,210],"prediction.":[24,211],"Especially,":[25],"estimating":[26],"a":[30,39,45,56,62,76,85,182,199],"single":[31,204],"model,":[33],"which":[34],"is":[35,54,102,198,224],"important":[36],"few":[40],"good":[41,178],"out":[43],"large":[46,106,183],"model":[47,86,155,205],"pool":[48],"consisting":[49,108],"mostly":[51,188],"low-quality":[52],"models,":[53],"still":[55],"largely":[57],"unsolved":[58],"problem.":[59],"We":[60],"introduce":[61],"novel":[63],"single-model":[64],"method":[67,161],"DeepQA":[68,162,197,221],"based":[69],"on":[70,104,152,167],"deep":[71,99,138],"belief":[72,100,139],"network":[73,101,140],"that":[74,137],"utilizes":[75],"number":[77],"selected":[79],"features":[80],"describing":[81],"from":[87,111,181],"different":[88],"perspectives,":[89],"such":[90],"energy,":[92],"physio-chemical":[93],"characteristics,":[94],"structural":[96],"information.":[97],"The":[98,212],"trained":[103],"several":[105,121],"datasets":[107,219],"Critical":[113],"Assessment":[114],"Structure":[117],"Prediction":[118],"(CASP)":[119],"experiments,":[120],"publicly":[122],"available":[123,226],"datasets,":[124],"generated":[127,191],"our":[129,160],"in-house":[130],"ab":[131,193],"initio":[132,194],"method.":[133],"Our":[134],"experiment":[135],"demonstrate":[136],"better":[142],"performance":[143,166],"compared":[144],"to":[145,227],"Support":[146],"Vector":[147],"Machines":[148],"Neural":[150],"Networks":[151],"problem,":[158],"achieves":[163],"state-of-the-art":[165],"CASP11":[168],"dataset.":[169],"It":[170],"also":[171],"outperformed":[172],"two":[173],"well-established":[174],"methods":[175],"in":[176],"outlier":[179],"set":[184],"low":[189],"modeling":[195],"methods.":[196],"useful":[200],"tool":[201],"source":[213],"code,":[214],"executable,":[215],"document":[216],"training/test":[218],"Linux":[223],"freely":[225],"non-commercial":[228],"users":[229],"at":[230],"http://cactus.rnet.missouri.edu/DeepQA/.":[231]},"counts_by_year":[{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":2}],"updated_date":"2026-10-15T10:00:46.086208","created_date":"2019-06-27T00:00:00"}