{"id":"https://openalex.org/W2095269881","doi":"https://doi.org/10.1002/(sici)1520-684x(19991130)30:13<13::aid-scj2>3.0.co;2-7","title":"Prediction of protein structure classes and secondary structures by means of hidden Markov models","display_name":"Prediction of protein structure classes and secondary structures by means of hidden Markov models","publication_year":1999,"publication_date":"1999-11-30","ids":{"openalex":"https://openalex.org/W2095269881","doi":"https://doi.org/10.1002/(sici)1520-684x(19991130)30:13<13::aid-scj2>3.0.co;2-7","mag":"2095269881"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1520-684x(19991130)30:13<13::aid-scj2>3.0.co;2-7","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1520-684x(19991130)30:13<13::aid-scj2>3.0.co;2-7","pdf_url":null,"source":{"id":"https://openalex.org/S58208175","display_name":"Systems and Computers in Japan","issn_l":"0882-1666","issn":["0882-1666","1520-684X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Systems and Computers in Japan","raw_type":"journal-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/A5034413775","display_name":"Hiroshi Yoshikawa","orcid":"https://orcid.org/0000-0003-0624-6039"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroshi Yoshikawa","raw_affiliation_strings":["Department of Biotechnology, University of Tokyo, Tokyo, Japan 113-8657"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, University of Tokyo, Tokyo, Japan 113-8657","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069786759","display_name":"Mitsunori Ikeguchi","orcid":"https://orcid.org/0000-0003-3199-6931"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Mitsunori Ikeguchi","raw_affiliation_strings":["Department of Biotechnology, University of Tokyo, Tokyo, Japan 113-8657"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, University of Tokyo, Tokyo, Japan 113-8657","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059004826","display_name":"Shugo Nakamura","orcid":"https://orcid.org/0000-0003-0851-7437"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Shugo Nakamura","raw_affiliation_strings":["Department of Biotechnology, University of Tokyo, Tokyo, Japan 113-8657"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, University of Tokyo, Tokyo, Japan 113-8657","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102746753","display_name":"Kentaro Shimizu","orcid":"https://orcid.org/0000-0002-3245-0052"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kentaro Shimizu","raw_affiliation_strings":["Department of Biotechnology, University of Tokyo, Tokyo, Japan 113-8657"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, University of Tokyo, Tokyo, Japan 113-8657","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010686893","display_name":"Junta Doi","orcid":null},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Junta Doi","raw_affiliation_strings":["Department of Biotechnology, University of Tokyo, Tokyo, Japan 113-8657"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, University of Tokyo, Tokyo, Japan 113-8657","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.11065758,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"30","issue":"13","first_page":"13","last_page":"22"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998999834060669,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998999834060669,"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":0.9997000098228455,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9983999729156494,"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/hidden-markov-model","display_name":"Hidden Markov model","score":0.866282045841217},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.8293501734733582},{"id":"https://openalex.org/keywords/protein-tertiary-structure","display_name":"Protein tertiary structure","score":0.7251503467559814},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5937139391899109},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.5875833034515381},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5847797393798828},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5732720494270325},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.564653217792511},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.4883860945701599},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4738338887691498},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4494016170501709},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.42861407995224},{"id":"https://openalex.org/keywords/structural-classification-of-proteins-database","display_name":"Structural Classification of Proteins database","score":0.4223201274871826},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38474711775779724},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3298787474632263},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.24032041430473328},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1580469012260437},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07734853029251099}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.866282045841217},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.8293501734733582},{"id":"https://openalex.org/C75599170","wikidata":"https://www.wikidata.org/wiki/Q898483","display_name":"Protein tertiary structure","level":2,"score":0.7251503467559814},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5937139391899109},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.5875833034515381},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5847797393798828},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5732720494270325},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.564653217792511},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.4883860945701599},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4738338887691498},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4494016170501709},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.42861407995224},{"id":"https://openalex.org/C58773245","wikidata":"https://www.wikidata.org/wiki/Q4832556","display_name":"Structural Classification of Proteins database","level":3,"score":0.4223201274871826},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38474711775779724},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3298787474632263},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.24032041430473328},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1580469012260437},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07734853029251099},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/(sici)1520-684x(19991130)30:13<13::aid-scj2>3.0.co;2-7","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1520-684x(19991130)30:13<13::aid-scj2>3.0.co;2-7","pdf_url":null,"source":{"id":"https://openalex.org/S58208175","display_name":"Systems and Computers in Japan","issn_l":"0882-1666","issn":["0882-1666","1520-684X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Systems and Computers in Japan","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W29708951","https://openalex.org/W1575431606","https://openalex.org/W1821507858","https://openalex.org/W1985818354","https://openalex.org/W1989447327","https://openalex.org/W1991133427","https://openalex.org/W2003685971","https://openalex.org/W2007569291","https://openalex.org/W2008708467","https://openalex.org/W2012515247","https://openalex.org/W2013136212","https://openalex.org/W2013570924","https://openalex.org/W2015328208","https://openalex.org/W2015532430","https://openalex.org/W2032005922","https://openalex.org/W2035066314","https://openalex.org/W2048102092","https://openalex.org/W2071764390","https://openalex.org/W2077574412","https://openalex.org/W2081359387","https://openalex.org/W2085277871","https://openalex.org/W2086699924","https://openalex.org/W2099302461","https://openalex.org/W2102122585","https://openalex.org/W2103334638","https://openalex.org/W2125838338","https://openalex.org/W2137995988","https://openalex.org/W2142384583","https://openalex.org/W2168211076","https://openalex.org/W2171901005","https://openalex.org/W2527367997","https://openalex.org/W3150945973","https://openalex.org/W4250384461","https://openalex.org/W6675645031","https://openalex.org/W6678068712","https://openalex.org/W6726339012","https://openalex.org/W6727660031"],"related_works":["https://openalex.org/W2010477190","https://openalex.org/W2059363535","https://openalex.org/W2037794263","https://openalex.org/W4206825711","https://openalex.org/W2494604670","https://openalex.org/W2114568928","https://openalex.org/W2554497004","https://openalex.org/W2052981282","https://openalex.org/W2095269881","https://openalex.org/W1789072987"],"abstract_inverted_index":{"This":[0],"study":[1],"deals":[2],"with":[3],"structure":[4,6,61,85,148,157],"class/secondary":[5],"prediction":[7,19,138,154],"of":[8,32,54,59,66,69,83,124,139,155,175],"proteins":[9],"using":[10,22],"hidden":[11],"Markov":[12],"models":[13],"(HMMs).":[14],"With":[15],"the":[16,75,88,103,137,167],"proposed":[17,168],"method,":[18],"is":[20,62,78,91,100],"performed":[21],"HMMs":[23,130],"designed":[24,131],"so":[25,73,107],"as":[26,132],"to":[27,127,136,171],"represent":[28],"hierarchicality":[29,58],"and":[30,117,163],"periodicity":[31,99],"protein":[33,60,176],"structural":[34,110,177],"features.":[35,178],"Secondary":[36],"structures":[37,49],"(partial":[38],"tertiary":[39,48,76],"structures)":[40],"are":[41,50,120],"formed":[42,51],"from":[43,80,93],"amino":[44,94],"acid":[45,95],"sequences":[46],"while":[47,87],"through":[52,122],"packing":[53],"secondary":[55,84,89,156],"structures;":[56],"thus,":[57],"represented":[63],"by":[64],"means":[65],"hierarchical":[67],"combination":[68],"multiple":[70],"HMMs.":[71],"In":[72,97],"doing,":[74],"HMM":[77,90,104],"built":[79,92],"a":[81],"sequence":[82],"segments":[86],"sequences.":[96],"addition,":[98],"introduced":[101],"into":[102],"network":[105],"topology":[106],"that":[108],"periodical":[109],"features":[111],"can":[112],"be":[113],"represented.":[114],"Transition":[115],"probabilities":[116,119],"output":[118],"determined":[121],"learning":[123],"data":[125],"related":[126],"known":[128],"structures.":[129,141],"mentioned":[133],"were":[134],"applied":[135],"unknown":[140],"Accuracy":[142],"above":[143],"50%":[144],"was":[145,158],"achieved":[146],"for":[147,160],"class":[149,162],"prediction.":[150],"Besides,":[151],"high":[152],"accuracy":[153],"obtained":[159],"\u03b1":[161],"\u03b1/\u03b2":[164],"class.":[165],"Thus,":[166],"method":[169],"proved":[170],"offer":[172],"faithful":[173],"representation":[174],"\u00a9":[179],"1999":[180,188],"Scripta":[181],"Technica,":[182],"Syst":[183],"Comp":[184],"Jpn,":[185],"30(13):":[186],"13\u201322,":[187]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
