{"id":"https://openalex.org/W1826484537","doi":"https://doi.org/10.1093/nar/gkv494","title":"CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts","display_name":"CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts","publication_year":2015,"publication_date":"2015-05-15","ids":{"openalex":"https://openalex.org/W1826484537","doi":"https://doi.org/10.1093/nar/gkv494","mag":"1826484537","pmid":"https://pubmed.ncbi.nlm.nih.gov/25979265"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkv494","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv494","pdf_url":"https://academic.oup.com/nar/article-pdf/43/W1/W370/7476377/gkv494.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","license_id":"https://openalex.org/licenses/cc-by","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/43/W1/W370/7476377/gkv494.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077540771","display_name":"Noor E. Hafsa","orcid":"https://orcid.org/0000-0002-8288-1782"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Noor E. Hafsa","raw_affiliation_strings":["Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada","institution_ids":["https://openalex.org/I154425047"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057343389","display_name":"David Arndt","orcid":"https://orcid.org/0000-0003-0703-8469"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"David Arndt","raw_affiliation_strings":["Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada","institution_ids":["https://openalex.org/I154425047"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003573061","display_name":"David S. Wishart","orcid":"https://orcid.org/0000-0002-3207-2434"},"institutions":[{"id":"https://openalex.org/I154425047","display_name":"University of Alberta","ror":"https://ror.org/0160cpw27","country_code":"CA","type":"education","lineage":["https://openalex.org/I154425047"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"David S. Wishart","raw_affiliation_strings":["Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada david.wishart@ualberta.ca","Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada","Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada david.wishart@ualberta.ca","institution_ids":[]},{"raw_affiliation_string":"Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada","institution_ids":["https://openalex.org/I154425047"]},{"raw_affiliation_string":"Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada","institution_ids":["https://openalex.org/I154425047"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5003573061"],"corresponding_institution_ids":["https://openalex.org/I154425047"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":6.9288,"has_fulltext":true,"cited_by_count":173,"citation_normalized_percentile":{"value":0.97594918,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"43","issue":"W1","first_page":"W370","last_page":"W377"},"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/T11162","display_name":"Enzyme Structure and Function","score":0.9998000264167786,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9857000112533569,"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/protein-secondary-structure","display_name":"Protein secondary structure","score":0.9092615842819214},{"id":"https://openalex.org/keywords/chemical-shift","display_name":"Chemical shift","score":0.6099523901939392},{"id":"https://openalex.org/keywords/intrinsically-disordered-proteins","display_name":"Intrinsically disordered proteins","score":0.5704402327537537},{"id":"https://openalex.org/keywords/nuclear-magnetic-resonance-spectroscopy","display_name":"Nuclear magnetic resonance spectroscopy","score":0.4808233976364136},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.42098289728164673},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40224123001098633},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.39510250091552734},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.34672683477401733},{"id":"https://openalex.org/keywords/nuclear-magnetic-resonance","display_name":"Nuclear magnetic resonance","score":0.3250827193260193},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.18977904319763184},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1335919201374054}],"concepts":[{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.9092615842819214},{"id":"https://openalex.org/C111429119","wikidata":"https://www.wikidata.org/wiki/Q899127","display_name":"Chemical shift","level":2,"score":0.6099523901939392},{"id":"https://openalex.org/C2778815515","wikidata":"https://www.wikidata.org/wiki/Q3408242","display_name":"Intrinsically disordered proteins","level":2,"score":0.5704402327537537},{"id":"https://openalex.org/C66974803","wikidata":"https://www.wikidata.org/wiki/Q10359898","display_name":"Nuclear magnetic resonance spectroscopy","level":2,"score":0.4808233976364136},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.42098289728164673},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40224123001098633},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.39510250091552734},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.34672683477401733},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.3250827193260193},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.18977904319763184},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1335919201374054}],"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":"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":"D019906","descriptor_name":"Nuclear Magnetic Resonance, Biomolecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019906","descriptor_name":"Nuclear Magnetic Resonance, Biomolecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019906","descriptor_name":"Nuclear Magnetic Resonance, Biomolecular","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkv494","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv494","pdf_url":"https://academic.oup.com/nar/article-pdf/43/W1/W370/7476377/gkv494.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:25979265","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25979265","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:europepmc.org:3458145","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4489240","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkv494","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkv494","pdf_url":"https://academic.oup.com/nar/article-pdf/43/W1/W370/7476377/gkv494.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320326646","display_name":"Genome Alberta","ror":null},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1826484537.pdf","grobid_xml":"https://content.openalex.org/works/W1826484537.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W145581483","https://openalex.org/W199186236","https://openalex.org/W1491642680","https://openalex.org/W1513002528","https://openalex.org/W1554093359","https://openalex.org/W1965151258","https://openalex.org/W1978545297","https://openalex.org/W1980897963","https://openalex.org/W1995987908","https://openalex.org/W1996367667","https://openalex.org/W2004405255","https://openalex.org/W2008708467","https://openalex.org/W2011148270","https://openalex.org/W2026469255","https://openalex.org/W2070534813","https://openalex.org/W2074655761","https://openalex.org/W2085705066","https://openalex.org/W2088848851","https://openalex.org/W2104226349","https://openalex.org/W2112418305","https://openalex.org/W2113403117","https://openalex.org/W2134455806","https://openalex.org/W2141920771","https://openalex.org/W2148521301","https://openalex.org/W2153187042","https://openalex.org/W2167785149","https://openalex.org/W2170671445","https://openalex.org/W2170823043","https://openalex.org/W2317622970","https://openalex.org/W2949250147"],"related_works":["https://openalex.org/W4293203577","https://openalex.org/W2038663961","https://openalex.org/W4288038979","https://openalex.org/W2964159616","https://openalex.org/W2969721268","https://openalex.org/W2041909424","https://openalex.org/W2573983130","https://openalex.org/W2898049514","https://openalex.org/W4385651120","https://openalex.org/W2032227844"],"abstract_inverted_index":{"The":[0,125],"Chemical":[1],"Shift":[2],"Index":[3],"or":[4,138],"CSI":[5,58,95,117,148,204],"3.0":[6,59,96,149],"(http://csi3.wishartlab.com)":[7],"is":[8],"a":[9,151],"web":[10],"server":[11],"designed":[12],"to":[13,159],"accurately":[14],"identify":[15,160],"the":[16,139,161],"location":[17],"of":[18,44,51,63,66,153],"secondary":[19,52,67,162,171],"and":[20,35,56,68,84,92,112,114,121,136,146,163,172,186,195],"super-secondary":[21,69,164,173],"structures":[22,165,191],"in":[23,103,166],"protein":[24,38,167,190],"chains":[25],"using":[26],"only":[27,47],"nuclear":[28],"magnetic":[29],"resonance":[30],"(NMR)":[31],"backbone":[32],"chemical":[33,100],"shifts":[34],"their":[36],"corresponding":[37],"sequence":[39],"data.":[40],"Unlike":[41],"earlier":[42],"versions":[43],"CSI,":[45],"which":[46],"identified":[48],"three":[49],"types":[50,65],"structure":[53,123,134,174],"(helix,":[54],"\u03b2-strand":[55],"coil),":[57],"now":[60],"identifies":[61],"total":[62],"11":[64],"structures,":[70],"including":[71],"helices,":[72],"\u03b2-strands,":[73],"coil":[74],"regions,":[75],"five":[76],"common":[77],"\u03b2-turns":[78],"(type":[79],"I,":[80],"II,":[81],"I',":[82],"II'":[83],"VIII),":[85],"\u03b2":[86],"hairpins":[87],"as":[88,90,131,183],"well":[89],"interior":[91],"edge":[93],"\u03b2-strands.":[94],"accepts":[97],"experimental":[98],"NMR":[99,109,196],"shift":[101],"data":[102],"multiple":[104],"formats":[105],"(NMR":[106],"Star":[107,110],"2.1,":[108],"3.1":[111],"SHIFTY)":[113],"generates":[115],"colorful":[116],"plots":[118],"(bar":[119],"graphs)":[120],"secondary/super-secondary":[122],"assignments.":[124],"output":[126],"can":[127],"be":[128,142],"readily":[129],"used":[130,143],"constraints":[132],"for":[133,144],"determination":[135],"refinement":[137],"images":[140],"may":[141],"presentations":[145],"publications.":[147],"uses":[150],"pipeline":[152],"several":[154],"well-tested,":[155],"previously":[156],"published":[157],"programs":[158,181],"chains.":[168],"Comparisons":[169],"with":[170,203],"assignments":[175],"made":[176,202],"via":[177],"standard":[178],"coordinate":[179],"analysis":[180],"such":[182],"DSSP,":[184],"STRIDE":[185],"VADAR":[187],"on":[188],"high-resolution":[189],"solved":[192],"by":[193],"X-ray":[194],"show":[197],">90%":[198],"agreement":[199],"between":[200],"those":[201],"3.0.":[205]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":24},{"year":2020,"cited_by_count":19},{"year":2019,"cited_by_count":19},{"year":2018,"cited_by_count":21},{"year":2017,"cited_by_count":16},{"year":2016,"cited_by_count":8}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}