{"id":"https://openalex.org/W2577244089","doi":"https://doi.org/10.1109/bibm.2016.7822781","title":"Selecting near-native structures from decoys using maximal cliques","display_name":"Selecting near-native structures from decoys using maximal cliques","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2577244089","doi":"https://doi.org/10.1109/bibm.2016.7822781","mag":"2577244089"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2016.7822781","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822781","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5100989024","display_name":"Jinyang Yan","orcid":null},"institutions":[{"id":"https://openalex.org/I76214153","display_name":"Lanzhou University","ror":"https://ror.org/01mkqqe32","country_code":"CN","type":"education","lineage":["https://openalex.org/I76214153"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinyang Yan","raw_affiliation_strings":["School of Information Science and Engineering, Lanzhou University, Lanzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Lanzhou University, Lanzhou, China","institution_ids":["https://openalex.org/I76214153"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082133960","display_name":"Yonggang Lu","orcid":"https://orcid.org/0000-0001-8926-2039"},"institutions":[{"id":"https://openalex.org/I76214153","display_name":"Lanzhou University","ror":"https://ror.org/01mkqqe32","country_code":"CN","type":"education","lineage":["https://openalex.org/I76214153"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yonggang Lu","raw_affiliation_strings":["School of Information Science and Engineering, Lanzhou University, Lanzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Lanzhou University, Lanzhou, China","institution_ids":["https://openalex.org/I76214153"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049641499","display_name":"Jing He","orcid":"https://orcid.org/0000-0002-7249-4746"},"institutions":[{"id":"https://openalex.org/I81365321","display_name":"Old Dominion University","ror":"https://ror.org/04zjtrb98","country_code":"US","type":"education","lineage":["https://openalex.org/I81365321"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing He","raw_affiliation_strings":["Department of Computer Science, Old Dominion University, Norfolk, Virginia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Old Dominion University, Norfolk, Virginia, USA","institution_ids":["https://openalex.org/I81365321"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10815815,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"1","issue":null,"first_page":"1745","last_page":"1748"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.998199999332428,"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/computer-science","display_name":"Computer science","score":0.6394616961479187},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6140025854110718},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5912109613418579},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5271517634391785},{"id":"https://openalex.org/keywords/centroid","display_name":"Centroid","score":0.4884323179721832},{"id":"https://openalex.org/keywords/decoy","display_name":"Decoy","score":0.48315519094467163},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4310576319694519},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4245643615722656},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.360295832157135},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34730058908462524},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.308083713054657}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6394616961479187},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6140025854110718},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5912109613418579},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5271517634391785},{"id":"https://openalex.org/C146599234","wikidata":"https://www.wikidata.org/wiki/Q511093","display_name":"Centroid","level":2,"score":0.4884323179721832},{"id":"https://openalex.org/C2779179475","wikidata":"https://www.wikidata.org/wiki/Q3545649","display_name":"Decoy","level":3,"score":0.48315519094467163},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4310576319694519},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4245643615722656},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.360295832157135},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34730058908462524},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.308083713054657},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","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/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1109/bibm.2016.7822781","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822781","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:ir.lzu.edu.cn/:262010/189675","is_oa":false,"landing_page_url":"http://ir.lzu.edu.cn/handle/262010/189675","pdf_url":null,"source":{"id":"https://openalex.org/S4406923049","display_name":"Lanzhou University Institutional Repository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference article (CA)"},{"id":"pmh:oai:ir.lzu.edu.cn/:262010/396998","is_oa":false,"landing_page_url":"http://ir.lzu.edu.cn/handle/262010/396998","pdf_url":null,"source":{"id":"https://openalex.org/S4406923049","display_name":"Lanzhou University Institutional Repository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference article (CA)"},{"id":"pmh:oai:ir.lzu.edu.cn/:262010/303387","is_oa":false,"landing_page_url":"http://ir.lzu.edu.cn/handle/262010/303387","pdf_url":null,"source":{"id":"https://openalex.org/S4406923049","display_name":"Lanzhou University Institutional Repository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conferences"},{"id":"pmh:oai:ir.lzu.edu.cn/:262010/308057","is_oa":false,"landing_page_url":"http://ir.lzu.edu.cn/handle/262010/308057","pdf_url":null,"source":{"id":"https://openalex.org/S4406923049","display_name":"Lanzhou University Institutional Repository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conferences"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5299999713897705,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1567562836","https://openalex.org/W1977706988","https://openalex.org/W1987134040","https://openalex.org/W2013792107","https://openalex.org/W2017285544","https://openalex.org/W2037312364","https://openalex.org/W2052311847","https://openalex.org/W2052963427","https://openalex.org/W2089923519","https://openalex.org/W2102245393","https://openalex.org/W2152495216","https://openalex.org/W2155201844","https://openalex.org/W2161151688","https://openalex.org/W2164750034","https://openalex.org/W2216040507","https://openalex.org/W6654076295"],"related_works":["https://openalex.org/W2085025986","https://openalex.org/W3004912075","https://openalex.org/W2173669824","https://openalex.org/W2107127921","https://openalex.org/W2913065212","https://openalex.org/W2128046947","https://openalex.org/W1972108315","https://openalex.org/W2032576606","https://openalex.org/W2946599741","https://openalex.org/W3045029306"],"abstract_inverted_index":{"Protein":[0],"structure":[1,19,22,41,59,64],"prediction":[2],"is":[3,60,113],"one":[4],"of":[5,17,51,129,137],"the":[6,15,36,40,47,52,57,63,79,103,116,123,126,130,135,152,155,168],"most":[7],"important":[8,53],"subjects":[9],"in":[10,78,93],"computational":[11],"structural":[12],"biology.":[13],"In":[14],"process":[16],"protein":[18],"prediction,":[20],"many":[21],"decoys":[23,42,104],"are":[24,44,74,105,132,141],"obtained.":[25],"It":[26],"has":[27],"remained":[28],"an":[29],"unsolved":[30],"and":[31,110,134],"challenging":[32],"problem":[33],"to":[34,46,96,151],"select":[35,159],"best":[37],"model":[38],"from":[39],"that":[43],"closest":[45],"native":[48,169],"structure.":[49],"One":[50],"methods":[54,68,72],"for":[55],"selecting":[56],"near-native":[58,144,161],"by":[61],"clustering":[62,71],"decoys.":[65,124],"The":[66,100,146],"traditional":[67,153],"simply":[69],"use":[70],"which":[73,163],"usually":[75],"not":[76],"appropriate":[77],"high":[80],"dimensional":[81],"conformation":[82],"space.":[83],"Here":[84],"we":[85],"propose":[86],"a":[87,111],"method":[88,157],"based":[89],"on":[90],"maximal":[91,127,139],"cliques":[92,128,140],"graph":[94,112,131],"theory":[95],"solve":[97],"this":[98],"problem.":[99],"similarities":[101,166],"between":[102],"first":[106],"computed":[107],"using":[108,115],"TM-score,":[109],"built":[114],"shared":[117],"nearest":[118],"neighbor":[119],"(SNN)":[120],"information":[121],"among":[122],"Then":[125],"found":[133],"centroids":[136],"these":[138],"selected":[142],"as":[143],"structures.":[145,170],"experiments":[147],"show":[148],"that,":[149],"compared":[150],"methods,":[154],"proposed":[156],"can":[158],"better":[160],"structures":[162],"have":[164],"higher":[165],"with":[167]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}