{"id":"https://openalex.org/W2028258513","doi":"https://doi.org/10.1021/ci5000856","title":"Protein Secondary Structure Classification Revisited: Processing DSSP Information with PSSC","display_name":"Protein Secondary Structure Classification Revisited: Processing DSSP Information with PSSC","publication_year":2014,"publication_date":"2014-05-28","ids":{"openalex":"https://openalex.org/W2028258513","doi":"https://doi.org/10.1021/ci5000856","mag":"2028258513","pmid":"https://pubmed.ncbi.nlm.nih.gov/24866861"},"language":"en","primary_location":{"id":"doi:10.1021/ci5000856","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci5000856","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5070899426","display_name":"Jan Zacharias","orcid":null},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jan Zacharias","raw_affiliation_strings":["Fachbereich Biologie, Chemie,\rPharmazie/Institute of Chemistry and Biochemistry, Freie Universit\u00e4t Berlin, Fabeckstrasse 36A, 14195 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Fachbereich Biologie, Chemie,\rPharmazie/Institute of Chemistry and Biochemistry, Freie Universit\u00e4t Berlin, Fabeckstrasse 36A, 14195 Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024132636","display_name":"Ernst\u2010Walter Knapp","orcid":null},"institutions":[{"id":"https://openalex.org/I75951250","display_name":"Freie Universit\u00e4t Berlin","ror":"https://ror.org/046ak2485","country_code":"DE","type":"education","lineage":["https://openalex.org/I75951250"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ernst-Walter Knapp","raw_affiliation_strings":["Fachbereich Biologie, Chemie,\rPharmazie/Institute of Chemistry and Biochemistry, Freie Universit\u00e4t Berlin, Fabeckstrasse 36A, 14195 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Fachbereich Biologie, Chemie,\rPharmazie/Institute of Chemistry and Biochemistry, Freie Universit\u00e4t Berlin, Fabeckstrasse 36A, 14195 Berlin, Germany","institution_ids":["https://openalex.org/I75951250"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5070899426"],"corresponding_institution_ids":["https://openalex.org/I75951250"],"apc_list":null,"apc_paid":null,"fwci":0.5577,"has_fulltext":false,"cited_by_count":44,"citation_normalized_percentile":{"value":0.65964394,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"54","issue":"7","first_page":"2166","last_page":"2179"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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/T11162","display_name":"Enzyme Structure and Function","score":0.9997000098228455,"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":0.9929999709129333,"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":0.5596411824226379},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3415709137916565},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3207132816314697}],"concepts":[{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.5596411824226379},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3415709137916565},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3207132816314697},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","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":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci5000856","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci5000856","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:24866861","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24866861","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W89038067","https://openalex.org/W1573702687","https://openalex.org/W1966345796","https://openalex.org/W1971251199","https://openalex.org/W1996073320","https://openalex.org/W2008708467","https://openalex.org/W2012334384","https://openalex.org/W2020960844","https://openalex.org/W2026258231","https://openalex.org/W2029667189","https://openalex.org/W2035352107","https://openalex.org/W2045032792","https://openalex.org/W2047572594","https://openalex.org/W2049902088","https://openalex.org/W2059089461","https://openalex.org/W2062668585","https://openalex.org/W2064323950","https://openalex.org/W2066805041","https://openalex.org/W2074986801","https://openalex.org/W2083753880","https://openalex.org/W2083816365","https://openalex.org/W2108067237","https://openalex.org/W2108921801","https://openalex.org/W2113381945","https://openalex.org/W2114850508","https://openalex.org/W2117898316","https://openalex.org/W2122468718","https://openalex.org/W2124323896","https://openalex.org/W2125725297","https://openalex.org/W2126103104","https://openalex.org/W2127793522","https://openalex.org/W2130479394","https://openalex.org/W2133657429","https://openalex.org/W2135815490","https://openalex.org/W2139236413","https://openalex.org/W2141920771","https://openalex.org/W2151960293","https://openalex.org/W2158714788","https://openalex.org/W2159427685","https://openalex.org/W2160050027","https://openalex.org/W2160512128","https://openalex.org/W2166414585","https://openalex.org/W2168172687","https://openalex.org/W2170711116","https://openalex.org/W2202461091"],"related_works":["https://openalex.org/W2935759653","https://openalex.org/W3105167352","https://openalex.org/W54078636","https://openalex.org/W2954470139","https://openalex.org/W1501425562","https://openalex.org/W2902782467","https://openalex.org/W3084825885","https://openalex.org/W2298861036","https://openalex.org/W3148032049","https://openalex.org/W2271181815"],"abstract_inverted_index":{"A":[0],"first":[1],"step":[2],"toward":[3],"three-dimensional":[4],"protein":[5,102,227],"structure":[6,21,81,104,204],"description":[7,51],"is":[8,38,52,90,136],"the":[9,46,79,124,168,182,191,211,218],"characterization":[10,82,105],"of":[11,45,83,111,129,141],"secondary":[12,20,103,142,203],"structure.":[13,170],"The":[14,127],"most":[15,61],"widely":[16],"used":[17],"program":[18],"for":[19,109,224],"assignment":[22,165,173],"remains":[23],"DSSP,":[24],"introduced":[25,130],"in":[26,39,132,144,181,186],"1983,":[27],"with":[28,158,163,174,190,207],"currently":[29],"more":[30,66,119,225],"than":[31,70,122],"400":[32],"citations":[33],"per":[34],"year.":[35],"DSSP":[36,59,84,134,175,219],"output":[37],"a":[40,151],"one-letter":[41],"representation,":[42],"where":[43],"much":[44],"information":[47,135],"on":[48,167],"DSSP's":[49],"internal":[50,80],"lost.":[53],"Recently":[54],"it":[55],"became":[56],"evident":[57],"that":[58,89,184],"overlooks":[60],"\u03c0-helical":[62,120],"structures,":[63],"which":[64],"are":[65,185],"prevalent":[67],"and":[68,92,209,222],"important":[69],"anticipated":[71],"before.":[72],"We":[73,98,195],"introduce":[74],"an":[75,86,164],"alternative":[76],"concept,":[77],"representing":[78],"as":[85],"eight-character":[87],"string":[88],"human-interpretable":[91],"easy":[93],"to":[94],"parse":[95],"by":[96,138,179],"software.":[97],"demonstrate":[99,196],"how":[100,197],"our":[101],"(PSSC)":[106],"code":[107,221],"allows":[108,223],"inspection":[110],"complicated":[112],"structural":[113],"features.":[114],"It":[115],"recognizes":[116],"ten":[117],"times":[118],"residues":[121,180],"does":[123],"standard":[125],"DSSP.":[126],"plausibility":[128],"changes":[131],"interpreting":[133],"demonstrated":[137],"better":[139],"clustering":[140],"structures":[143],"(\u03c6,":[145],"\u03c8)":[146],"dihedral":[147],"angle":[148],"space.":[149],"With":[150],"sliding":[152],"sequence":[153],"window":[154],"(SSW),":[155],"helical":[156],"assignments":[157],"PSSC":[159,208],"remain":[160],"invariant":[161],"compared":[162],"based":[166],"complete":[169],"In":[171],"contrast,":[172],"can":[176,199],"be":[177],"changed":[178],"neighborhood":[183],"fact":[187],"not":[188],"interacting":[189],"residue":[192],"under":[193],"consideration.":[194],"one":[198],"easily":[200],"define":[201],"new":[202],"classification":[205],"schemes":[206],"perform":[210],"classifications.":[212],"Our":[213],"approach":[214],"works":[215],"without":[216],"changing":[217],"source":[220],"detailed":[226],"characterization.":[228]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
