{"id":"https://openalex.org/W1966279573","doi":"https://doi.org/10.1109/grc.2012.6468600","title":"A nearest neighbor method for predicting solenoid proteins","display_name":"A nearest neighbor method for predicting solenoid proteins","publication_year":2012,"publication_date":"2012-08-01","ids":{"openalex":"https://openalex.org/W1966279573","doi":"https://doi.org/10.1109/grc.2012.6468600","mag":"1966279573"},"language":"en","primary_location":{"id":"doi:10.1109/grc.2012.6468600","is_oa":false,"landing_page_url":"https://doi.org/10.1109/grc.2012.6468600","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Granular Computing","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/A5027972648","display_name":"Wen Cheng","orcid":null},"institutions":[{"id":"https://openalex.org/I57328836","display_name":"North Dakota State University","ror":"https://ror.org/05h1bnb22","country_code":"US","type":"education","lineage":["https://openalex.org/I57328836"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wen Cheng","raw_affiliation_strings":["Department of Computer Science, North Dakota State University, Fargo, ND, USA","Department of Computer Science, North Dakota State University Fargo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, North Dakota State University, Fargo, ND, USA","institution_ids":["https://openalex.org/I57328836"]},{"raw_affiliation_string":"Department of Computer Science, North Dakota State University Fargo, USA","institution_ids":["https://openalex.org/I57328836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064805230","display_name":"Malinda Vikum Sanjaka","orcid":null},"institutions":[{"id":"https://openalex.org/I57328836","display_name":"North Dakota State University","ror":"https://ror.org/05h1bnb22","country_code":"US","type":"education","lineage":["https://openalex.org/I57328836"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Malinda Sanjaka","raw_affiliation_strings":["Department of Computer Science, North Dakota State University, Fargo, ND, USA","Department of Computer Science, North Dakota State University Fargo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, North Dakota State University, Fargo, ND, USA","institution_ids":["https://openalex.org/I57328836"]},{"raw_affiliation_string":"Department of Computer Science, North Dakota State University Fargo, USA","institution_ids":["https://openalex.org/I57328836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100871727","display_name":"Changhui Yan","orcid":"https://orcid.org/0000-0003-3048-8628"},"institutions":[{"id":"https://openalex.org/I57328836","display_name":"North Dakota State University","ror":"https://ror.org/05h1bnb22","country_code":"US","type":"education","lineage":["https://openalex.org/I57328836"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Changhui Yan","raw_affiliation_strings":["Department of Computer Science, North Dakota State University, Fargo, ND, USA","Department of Computer Science, North Dakota State University Fargo, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, North Dakota State University, Fargo, ND, USA","institution_ids":["https://openalex.org/I57328836"]},{"raw_affiliation_string":"Department of Computer Science, North Dakota State University Fargo, USA","institution_ids":["https://openalex.org/I57328836"]}]}],"institutions":[],"countries_distinct_count":1,"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":0.0556015,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":null,"first_page":"68","last_page":"71"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9993000030517578,"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":0.9993000030517578,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9988999962806702,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955000281333923,"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/solenoid","display_name":"Solenoid","score":0.6705617308616638},{"id":"https://openalex.org/keywords/euclidean-distance","display_name":"Euclidean distance","score":0.653383731842041},{"id":"https://openalex.org/keywords/k-nearest-neighbors-algorithm","display_name":"k-nearest neighbors algorithm","score":0.5907167196273804},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.45265477895736694},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4362723231315613},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35486701130867004},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3159196078777313},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20915070176124573},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.17831337451934814}],"concepts":[{"id":"https://openalex.org/C192144188","wikidata":"https://www.wikidata.org/wiki/Q245739","display_name":"Solenoid","level":2,"score":0.6705617308616638},{"id":"https://openalex.org/C120174047","wikidata":"https://www.wikidata.org/wiki/Q847073","display_name":"Euclidean distance","level":2,"score":0.653383731842041},{"id":"https://openalex.org/C113238511","wikidata":"https://www.wikidata.org/wiki/Q1071612","display_name":"k-nearest neighbors algorithm","level":2,"score":0.5907167196273804},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.45265477895736694},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4362723231315613},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35486701130867004},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3159196078777313},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20915070176124573},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.17831337451934814},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/grc.2012.6468600","is_oa":false,"landing_page_url":"https://doi.org/10.1109/grc.2012.6468600","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Granular Computing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W66352343","https://openalex.org/W1971650367","https://openalex.org/W1993166171","https://openalex.org/W2006819428","https://openalex.org/W2008560636","https://openalex.org/W2023167553","https://openalex.org/W2051119339","https://openalex.org/W2066688961","https://openalex.org/W2096929799","https://openalex.org/W2105961968","https://openalex.org/W2114914350","https://openalex.org/W2124658247","https://openalex.org/W2132505033","https://openalex.org/W2147595457","https://openalex.org/W2158714788","https://openalex.org/W2161151688","https://openalex.org/W2162085776"],"related_works":["https://openalex.org/W2990663423","https://openalex.org/W2062957446","https://openalex.org/W2166213322","https://openalex.org/W3171568022","https://openalex.org/W2099606355","https://openalex.org/W2147397890","https://openalex.org/W2155880659","https://openalex.org/W894329006","https://openalex.org/W2097149198","https://openalex.org/W2023878529"],"abstract_inverted_index":{"Solenoid":[0],"proteins":[1,3,15,38,46,65],"are":[2,24,97],"with":[4,66,72,92],"repeats":[5],"of":[6,70],"5":[7],"to":[8],"40":[9],"residues":[10],"in":[11,81,113],"length.":[12],"Identifying":[13],"solenoid":[14,37,64],"presents":[16],"a":[17,30,50],"big":[18],"challenge":[19],"because":[20],"the":[21,56,89,103,109],"repeat":[22],"sequences":[23],"highly":[25],"degenerated.":[26],"Here,":[27],"we":[28],"present":[29],"nearest":[31],"neighbor":[32],"(NN)":[33],"method":[34,62,91],"for":[35,101],"predicting":[36,114],"based":[39],"on":[40],"residue":[41,57],"composition.":[42],"The":[43,60],"distance":[44,53],"between":[45],"is":[47],"calculated":[48],"as":[49],"weighted":[51],"Euclidean":[52],"defined":[54],"by":[55],"composition":[58],"vector.":[59],"NN":[61,90],"predicts":[63],"an":[67],"overall":[68],"accuracy":[69],"95.5%":[71],"94.3%":[73],"sensitivity":[74],"and":[75,94],"96%":[76],"specificity,":[77],"outperforming":[78],"other":[79],"methods":[80,100],"direct":[82],"comparisons.":[83],"We":[84],"also":[85],"demonstrate":[86],"that":[87],"combining":[88],"HHrepID":[93],"Trust,":[95],"which":[96],"previously":[98],"published":[99],"addressing":[102],"same":[104],"problem,":[105],"can":[106],"dramatically":[107],"reduce":[108],"false":[110],"positive":[111],"rates":[112],"repeats.":[115]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
