{"id":"https://openalex.org/W2060178110","doi":"https://doi.org/10.1093/nar/gkn238","title":"The Jpred 3 secondary structure prediction server","display_name":"The Jpred 3 secondary structure prediction server","publication_year":2008,"publication_date":"2008-05-07","ids":{"openalex":"https://openalex.org/W2060178110","doi":"https://doi.org/10.1093/nar/gkn238","mag":"2060178110","pmid":"https://pubmed.ncbi.nlm.nih.gov/18463136"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkn238","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn238","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W197/7625322/gkn238.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W197/7625322/gkn238.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087385117","display_name":"Christian Cole","orcid":"https://orcid.org/0000-0002-2560-2484"},"institutions":[{"id":"https://openalex.org/I177639307","display_name":"University of Dundee","ror":"https://ror.org/03h2bxq36","country_code":"GB","type":"education","lineage":["https://openalex.org/I177639307"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"C. Cole","raw_affiliation_strings":["School of Life Sciences Research, University of Dundee, Dow Street, Dundee, DD1 5EH, UK","School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, UK"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences Research, University of Dundee, Dow Street, Dundee, DD1 5EH, UK","institution_ids":["https://openalex.org/I177639307"]},{"raw_affiliation_string":"School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, UK","institution_ids":["https://openalex.org/I177639307"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075807327","display_name":"Jonathan D. Barber","orcid":null},"institutions":[{"id":"https://openalex.org/I177639307","display_name":"University of Dundee","ror":"https://ror.org/03h2bxq36","country_code":"GB","type":"education","lineage":["https://openalex.org/I177639307"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"J. D. Barber","raw_affiliation_strings":["School of Life Sciences Research, University of Dundee, Dow Street, Dundee, DD1 5EH, UK","School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, UK"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences Research, University of Dundee, Dow Street, Dundee, DD1 5EH, UK","institution_ids":["https://openalex.org/I177639307"]},{"raw_affiliation_string":"School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, UK","institution_ids":["https://openalex.org/I177639307"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082043302","display_name":"Geoffrey J. Barton","orcid":"https://orcid.org/0000-0002-9014-5355"},"institutions":[{"id":"https://openalex.org/I177639307","display_name":"University of Dundee","ror":"https://ror.org/03h2bxq36","country_code":"GB","type":"education","lineage":["https://openalex.org/I177639307"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"G. J. Barton","raw_affiliation_strings":["School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, UK"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences Research, University of Dundee, Dow Street, Dundee DD1 5EH, UK","institution_ids":["https://openalex.org/I177639307"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5087385117"],"corresponding_institution_ids":["https://openalex.org/I177639307"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":74.3966,"has_fulltext":false,"cited_by_count":1442,"citation_normalized_percentile":{"value":0.99968794,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"36","issue":"Web Server","first_page":"W197","last_page":"W201"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9995999932289124,"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/T10044","display_name":"Protein Structure and Dynamics","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":0.996399998664856,"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/pipeline","display_name":"Pipeline (software)","score":0.7095840573310852},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.7094618082046509},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5674135088920593},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.5496049523353577},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5283563733100891},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.477407842874527},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4560052156448364},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.4559739828109741},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.4449373483657837},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.27351734042167664},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11825427412986755},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11112111806869507},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09596920013427734}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7095840573310852},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.7094618082046509},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5674135088920593},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.5496049523353577},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5283563733100891},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.477407842874527},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4560052156448364},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.4559739828109741},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.4449373483657837},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.27351734042167664},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11825427412986755},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11112111806869507},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09596920013427734},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkn238","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn238","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W197/7625322/gkn238.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:18463136","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18463136","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:discovery.dundee.ac.uk:openaire_cris_publications/0bdf816b-8431-42a3-a7ef-2870fb49de0b","is_oa":false,"landing_page_url":"https://discovery.dundee.ac.uk/en/publications/0bdf816b-8431-42a3-a7ef-2870fb49de0b","pdf_url":null,"source":{"id":"https://openalex.org/S4306400523","display_name":"Discovery Research Portal (University of Dundee)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177639307","host_organization_name":"University of Dundee","host_organization_lineage":["https://openalex.org/I177639307"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cole, C, Barber, J D & Barton, G J 2008, 'The Jpred 3 secondary structure prediction server', Nucleic Acids Research, vol. 36, no. S2, pp. W197-W201. https://doi.org/10.1093/nar/gkn238","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:2447793","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2447793","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkn238","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn238","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W197/7625322/gkn238.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.49000000953674316}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2060178110.pdf","grobid_xml":"https://content.openalex.org/works/W2060178110.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W129635393","https://openalex.org/W1542067597","https://openalex.org/W1606410455","https://openalex.org/W1969007008","https://openalex.org/W1985818354","https://openalex.org/W1987328021","https://openalex.org/W2004461664","https://openalex.org/W2014011595","https://openalex.org/W2024645073","https://openalex.org/W2052935924","https://openalex.org/W2053197719","https://openalex.org/W2055043387","https://openalex.org/W2057289558","https://openalex.org/W2061500593","https://openalex.org/W2076048958","https://openalex.org/W2085277871","https://openalex.org/W2091969321","https://openalex.org/W2095450147","https://openalex.org/W2110639454","https://openalex.org/W2119511059","https://openalex.org/W2130479394","https://openalex.org/W2139582206","https://openalex.org/W2141915739","https://openalex.org/W2145358391","https://openalex.org/W2148047088","https://openalex.org/W2148676725","https://openalex.org/W2151430326","https://openalex.org/W2151831732","https://openalex.org/W2153187042","https://openalex.org/W2156914590","https://openalex.org/W2158714788","https://openalex.org/W2161062388","https://openalex.org/W2170471837","https://openalex.org/W2530374949","https://openalex.org/W4211083314","https://openalex.org/W4230246035","https://openalex.org/W4236236547","https://openalex.org/W4256395558"],"related_works":["https://openalex.org/W24553703","https://openalex.org/W4211000692","https://openalex.org/W4212920271","https://openalex.org/W4211054902","https://openalex.org/W2612240612","https://openalex.org/W4324018414","https://openalex.org/W4211208250","https://openalex.org/W2472351724","https://openalex.org/W3145366215","https://openalex.org/W2993777277"],"abstract_inverted_index":{"Jpred":[0,13,59,102,163],"(http://www.compbio.dundee.ac.uk/jpred)":[1],"is":[2],"a":[3,33,50,55],"secondary":[4,41,67],"structure":[5,42,68],"prediction":[6,39],"server":[7,104],"powered":[8],"by":[9],"the":[10,87,98,114,135],"Jnet":[11,30],"algorithm.":[12],"performs":[14],"over":[15],"1000":[16],"predictions":[17,65,75],"per":[18],"week":[19],"for":[20],"users":[21],"in":[22,94,150],"more":[23],"than":[24],"50":[25],"countries.":[26],"The":[27,74,100],"recently":[28],"updated":[29,149],"algorithm":[31],"provides":[32],"three-state":[34],"(alpha-helix,":[35],"beta-strand":[36],"and":[37,69,85,96,132,157,159],"coil)":[38],"of":[40,46,66,113,118,126],"at":[43],"an":[44],"accuracy":[45],"81.5%.":[47],"Given":[48],"either":[49],"single":[51],"protein":[52],"sequence":[53,57],"or":[54,116],"multiple":[56],"alignment,":[58],"derives":[60],"alignment":[61,89],"profiles":[62],"from":[63],"which":[64],"solvent":[70],"accessibility":[71],"are":[72,76],"made.":[73],"presented":[77],"as":[78],"coloured":[79],"HTML,":[80],"plain":[81],"text,":[82],"PostScript,":[83],"PDF":[84],"via":[86,130],"Jalview":[88],"editor":[90],"to":[91,134,145,147,155],"allow":[92],"flexibility":[93],"viewing":[95],"applying":[97],"data.":[99],"new":[101,139],"3":[103,164],"includes":[105],"significant":[106],"usability":[107],"improvements":[108,122],"that":[109,162],"include":[110,123],"clearer":[111],"feedback":[112],"progress":[115],"failure":[117],"submitted":[119],"requests.":[120],"Functional":[121],"batch":[124],"submission":[125],"sequences,":[127],"summary":[128],"results":[129],"email":[131],"updates":[133,154],"search":[136],"databases.":[137],"A":[138],"software":[140],"pipeline":[141],"will":[142,165],"enable":[143],"Jnet/Jpred":[144],"continue":[146],"be":[148],"sync":[151],"with":[152],"major":[153],"SCOP":[156],"UniProt":[158],"so":[160],"ensures":[161],"maintain":[166],"high-accuracy":[167],"predictions.":[168]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":19},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":28},{"year":2020,"cited_by_count":36},{"year":2019,"cited_by_count":31},{"year":2018,"cited_by_count":39},{"year":2017,"cited_by_count":55},{"year":2016,"cited_by_count":74},{"year":2015,"cited_by_count":173},{"year":2014,"cited_by_count":178},{"year":2013,"cited_by_count":176},{"year":2012,"cited_by_count":162}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
