{"id":"https://openalex.org/W2142727530","doi":"https://doi.org/10.1002/(sici)1096-987x(19991115)20:14<1455::aid-jcc1>3.0.co;2-d","title":"Protein sequence threading, the alignment problem, and a two-step strategy","display_name":"Protein sequence threading, the alignment problem, and a two-step strategy","publication_year":1999,"publication_date":"1999-11-15","ids":{"openalex":"https://openalex.org/W2142727530","doi":"https://doi.org/10.1002/(sici)1096-987x(19991115)20:14<1455::aid-jcc1>3.0.co;2-d","mag":"2142727530"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1096-987x(19991115)20:14<1455::aid-jcc1>3.0.co;2-d","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19991115)20:14<1455::aid-jcc1>3.0.co;2-d","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"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":"Journal of Computational Chemistry","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/A5076677952","display_name":"Thomas Huber","orcid":"https://orcid.org/0000-0002-3680-8699"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Thomas Huber","raw_affiliation_strings":["ANU Supercomputing Facility, Australian National University, Canberra ACT 0200, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ANU Supercomputing Facility, Australian National University, Canberra ACT 0200, Australia","institution_ids":["https://openalex.org/I118347636"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002244022","display_name":"Andrew E. Torda","orcid":"https://orcid.org/0000-0002-6076-709X"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Andrew E. Torda","raw_affiliation_strings":["Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research School of Chemistry, Australian National University, Canberra ACT 0200, Australia","institution_ids":["https://openalex.org/I118347636"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5002244022"],"corresponding_institution_ids":["https://openalex.org/I118347636"],"apc_list":{"value":4520,"currency":"USD","value_usd":4520},"apc_paid":null,"fwci":0.6842,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.68172438,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"20","issue":"14","first_page":"1455","last_page":"1467"},"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/T11162","display_name":"Enzyme Structure and Function","score":0.9988999962806702,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9980000257492065,"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/threading","display_name":"Threading (protein sequence)","score":0.7686086893081665},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6192145347595215},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5608876347541809},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5252637267112732},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4883594214916229},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.46030619740486145},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4587898254394531},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.42700842022895813},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.4085288345813751},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.3651595115661621},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.34651732444763184},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.31261175870895386},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22014522552490234},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1533927023410797},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.13074266910552979},{"id":"https://openalex.org/keywords/pure-mathematics","display_name":"Pure mathematics","score":0.09316396713256836}],"concepts":[{"id":"https://openalex.org/C200307862","wikidata":"https://www.wikidata.org/wiki/Q7797175","display_name":"Threading (protein sequence)","level":3,"score":0.7686086893081665},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6192145347595215},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5608876347541809},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5252637267112732},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4883594214916229},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.46030619740486145},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4587898254394531},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.42700842022895813},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.4085288345813751},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.3651595115661621},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.34651732444763184},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.31261175870895386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22014522552490234},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1533927023410797},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.13074266910552979},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.09316396713256836},{"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/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","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":4,"locations":[{"id":"doi:10.1002/(sici)1096-987x(19991115)20:14<1455::aid-jcc1>3.0.co;2-d","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19991115)20:14<1455::aid-jcc1>3.0.co;2-d","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"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":"Journal of Computational Chemistry","raw_type":"journal-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.46.1197","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.46.1197","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.rsc.anu.edu.au/pub/torda/papers/threadpaper.ps.Z","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.5.9784","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.5.9784","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.zbh.uni-hamburg.de/research/BM/torda/papers/thread_jcc99.pdf","raw_type":"text"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:35933","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","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":47,"referenced_works":["https://openalex.org/W1503558940","https://openalex.org/W1965008830","https://openalex.org/W1965860531","https://openalex.org/W1974885083","https://openalex.org/W1986966735","https://openalex.org/W1993762285","https://openalex.org/W1994518388","https://openalex.org/W1996470926","https://openalex.org/W2001956250","https://openalex.org/W2008708467","https://openalex.org/W2014140912","https://openalex.org/W2016411902","https://openalex.org/W2021953523","https://openalex.org/W2025296354","https://openalex.org/W2027071679","https://openalex.org/W2033496784","https://openalex.org/W2034728433","https://openalex.org/W2040594319","https://openalex.org/W2041966417","https://openalex.org/W2047477476","https://openalex.org/W2047974333","https://openalex.org/W2050330741","https://openalex.org/W2053281575","https://openalex.org/W2056807348","https://openalex.org/W2068745373","https://openalex.org/W2073403131","https://openalex.org/W2074231493","https://openalex.org/W2076514152","https://openalex.org/W2077840524","https://openalex.org/W2080184519","https://openalex.org/W2082169035","https://openalex.org/W2082296224","https://openalex.org/W2082621844","https://openalex.org/W2085277871","https://openalex.org/W2087982379","https://openalex.org/W2096943217","https://openalex.org/W2133715954","https://openalex.org/W2135069437","https://openalex.org/W2136739161","https://openalex.org/W2137345862","https://openalex.org/W2139279375","https://openalex.org/W2155479906","https://openalex.org/W2164308539","https://openalex.org/W2165982110","https://openalex.org/W2168211076","https://openalex.org/W2171335714","https://openalex.org/W2330066387"],"related_works":["https://openalex.org/W2253761889","https://openalex.org/W2136856901","https://openalex.org/W1741740882","https://openalex.org/W2181585194","https://openalex.org/W3149404221","https://openalex.org/W2043066834","https://openalex.org/W2111643578","https://openalex.org/W1975681040","https://openalex.org/W1493412556","https://openalex.org/W1888349473"],"abstract_inverted_index":{"Conventionally,":[0],"protein":[1,14],"structure":[2,76],"prediction":[3],"via":[4],"\u201cthreading\u201d":[5],"relies":[6],"on":[7],"some":[8],"nonoptimal":[9],"method":[10,70,91],"to":[11,16,38,48,73,75,95,133],"align":[12],"a":[13,20,28,44,79,125,151],"sequence":[15,74],"each":[17],"member":[18],"of":[19,22,43,111,113,127],"library":[21],"known":[23],"structures.":[24],"We":[25],"show":[26],"how":[27],"score":[29,65,83,144,153],"function":[30,66,84,145,154],"(force":[31],"field)":[32],"can":[33,57,130,146],"be":[34,58,131,148],"modified":[35],"so":[36],"as":[37],"allow":[39],"the":[40,49,86,96,114,136,142,156],"direct":[41],"application":[42],"dynamic":[45],"programming":[46],"algorithm":[47],"problem.":[50],"This":[51],"involves":[52],"an":[53,61],"approximation":[54],"whose":[55],"damage":[56],"minimized":[59],"by":[60,141],"optimization":[62],"process":[63],"during":[64],"parameter":[67],"determination.":[68],"The":[69,89],"is":[71,100,108],"compared":[72],"alignments":[77],"using":[78,150],"more":[80],"conventional":[81],"pair-wise":[82],"and":[85,102,120],"frozen":[87,97,137],"approximation.":[88,138],"new":[90],"produces":[92],"results":[93],"comparable":[94],"approximation,":[98],"but":[99],"faster":[101],"has":[103],"fewer":[104],"adjustable":[105],"parameters.":[106],"It":[107],"also":[109],"free":[110],"memory":[112],"template's":[115],"original":[116],"amino":[117],"acid":[118],"sequence,":[119],"does":[121],"not":[122],"suffer":[123],"from":[124],"problem":[126],"nonconvergence,":[128],"which":[129],"shown":[132],"occur":[134],"with":[135,155],"Alignments":[139],"generated":[140],"simplified":[143],"then":[147],"ranked":[149],"second":[152],"approximations":[157],"removed.":[158],"\u00a91999":[159],"John":[160],"Wiley":[161],"&":[162],"Sons,":[163],"Inc.":[164],"J":[165],"Comput":[166],"Chem":[167],"20:":[168],"1455\u20131467,":[169],"1999":[170]},"counts_by_year":[{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
