{"id":"https://openalex.org/W2163205257","doi":"https://doi.org/10.1109/icassp.2004.1327176","title":"Protein secondary structure prediction with semi Markov HMMs","display_name":"Protein secondary structure prediction with semi Markov HMMs","publication_year":2004,"publication_date":"2004-09-28","ids":{"openalex":"https://openalex.org/W2163205257","doi":"https://doi.org/10.1109/icassp.2004.1327176","mag":"2163205257"},"language":"en","primary_location":{"id":"doi:10.1109/icassp.2004.1327176","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icassp.2004.1327176","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2004 IEEE International Conference on Acoustics, Speech, and Signal Processing","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/A5082103872","display_name":"Zafer Ayd\u0131n","orcid":"https://orcid.org/0000-0001-7686-6298"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Z. Aydin","raw_affiliation_strings":["Center for Signal and Image Processing, Georgia Institute of Technology, Atlanta, GA, USA"],"affiliations":[{"raw_affiliation_string":"Center for Signal and Image Processing, Georgia Institute of Technology, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083265370","display_name":"Y. Altunbasak","orcid":null},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Y. Altunbasak","raw_affiliation_strings":["Center for Signal and Image Processing, Georgia Institute of Technology, Atlanta, GA, USA"],"affiliations":[{"raw_affiliation_string":"Center for Signal and Image Processing, Georgia Institute of Technology, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057317686","display_name":"Mark Borodovsky","orcid":"https://orcid.org/0000-0002-1401-4046"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Borodovsky","raw_affiliation_strings":["Schools of Biology and Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA"],"affiliations":[{"raw_affiliation_string":"Schools of Biology and Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA","institution_ids":["https://openalex.org/I130701444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5082103872"],"corresponding_institution_ids":["https://openalex.org/I130701444"],"apc_list":null,"apc_paid":null,"fwci":1.0525,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.74820336,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"5","issue":null,"first_page":"V","last_page":"577"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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/T10044","display_name":"Protein Structure and Dynamics","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/T12254","display_name":"Machine Learning in Bioinformatics","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987000226974487,"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":0.8998477458953857},{"id":"https://openalex.org/keywords/dependency","display_name":"Dependency (UML)","score":0.6288477778434753},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5629624724388123},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.5342577695846558},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.5264885425567627},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5243018865585327},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4752996861934662},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45559218525886536},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.45507681369781494},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.43113973736763},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.42392563819885254},{"id":"https://openalex.org/keywords/markov-process","display_name":"Markov process","score":0.415780246257782},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.413967102766037},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.35690927505493164},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3524233102798462},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.30218392610549927},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.17083454132080078},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12833544611930847},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10164403915405273}],"concepts":[{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.8998477458953857},{"id":"https://openalex.org/C19768560","wikidata":"https://www.wikidata.org/wiki/Q320727","display_name":"Dependency (UML)","level":2,"score":0.6288477778434753},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5629624724388123},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5342577695846558},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5264885425567627},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5243018865585327},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4752996861934662},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45559218525886536},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.45507681369781494},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.43113973736763},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.42392563819885254},{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.415780246257782},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.413967102766037},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.35690927505493164},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3524233102798462},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.30218392610549927},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.17083454132080078},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12833544611930847},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10164403915405273},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"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/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/icassp.2004.1327176","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icassp.2004.1327176","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2004 IEEE International Conference on Acoustics, Speech, and Signal Processing","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":7,"referenced_works":["https://openalex.org/W89038067","https://openalex.org/W2002272439","https://openalex.org/W2008708467","https://openalex.org/W2085277871","https://openalex.org/W2125838338","https://openalex.org/W2133142974","https://openalex.org/W3047703793"],"related_works":["https://openalex.org/W2928838901","https://openalex.org/W2494604670","https://openalex.org/W1578077690","https://openalex.org/W1998289425","https://openalex.org/W1510508486","https://openalex.org/W2303656598","https://openalex.org/W3097079079","https://openalex.org/W4206825711","https://openalex.org/W2114568928","https://openalex.org/W3086268169"],"abstract_inverted_index":{"Secondary":[0],"structure":[1,11,40],"prediction":[2,70,94],"has":[3],"been":[4],"an":[5,131,152],"essential":[6],"task":[7],"in":[8,170],"determining":[9],"the":[10,23,38,64,69,89,103,118,142,158],"and":[12],"function":[13],"of":[14,91],"proteins.":[15],"Prediction":[16],"accuracy":[17,71],"is":[18,61],"improving":[19],"every":[20],"year":[21],"towards":[22],"estimated":[24],"88%":[25],"theoretical":[26],"limit":[27],"(Rost.":[28],"B.,":[29],"http://cubic.bioc.columbia.edu/papers/2002":[30],"rev":[31],"dekker/paper.html).":[32],"There":[33],"are":[34],"two":[35],"approaches":[36],"for":[37],"secondary":[39],"prediction.":[41],"The":[42,56],"first":[43],"one,":[44],"ab":[45],"initio":[46],"(single":[47],"sequence)":[48],"prediction,":[49],"does":[50],"not":[51],"use":[52],"any":[53],"homology":[54],"information.":[55],"evolutionary":[57],"information,":[58],"if":[59],"available,":[60],"used":[62],"by":[63,72,95,106,116],"second":[65],"approach":[66],"to":[67,102,137,144,156],"improve":[68],"a":[73,97,112],"few":[74],"percentages":[75],"(Schmidler,":[76],"S.C.":[77],"et":[78,108],"al.,":[79],"J.":[80],"Computational":[81],"Biology,":[82],"vol.7,":[83],"no.1/2,":[84],"p.233-48,":[85],"2000).":[86],"We":[87,110],"address":[88],"problem":[90],"single":[92],"sequence":[93],"developing":[96],"semi":[98],"Markov":[99],"HMM,":[100],"similar":[101],"one":[104],"proposed":[105],"Schmidler":[107],"al.":[109],"introduce":[111],"better":[113],"dependency":[114,133],"model":[115,134],"considering":[117,135],"statistically":[119],"significant":[120],"amino":[121],"acid":[122],"correlation":[123],"patterns":[124],"at":[125],"segment":[126],"borders.":[127],"Also,":[128],"we":[129,150,166],"propose":[130,151],"internal":[132],"right":[136,145],"left":[138,143],"dependencies":[139],"without":[140],"modifying":[141],"HMM":[146,159],"topology.":[147],"In":[148],"addition,":[149],"iterative":[153],"training":[154],"method":[155],"estimate":[157],"parameters":[160],"better.":[161],"Putting":[162],"all":[163],"these":[164],"together,":[165],"obtained":[167],"1.5%":[168],"improvement":[169],"three-state-per-residue":[171],"accuracy.":[172]},"counts_by_year":[{"year":2017,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
