{"id":"https://openalex.org/W1969436613","doi":"https://doi.org/10.1093/nar/gkg110","title":"The PSSH database of alignments between protein sequences and tertiary structures","display_name":"The PSSH database of alignments between protein sequences and tertiary structures","publication_year":2003,"publication_date":"2003-01-01","ids":{"openalex":"https://openalex.org/W1969436613","doi":"https://doi.org/10.1093/nar/gkg110","mag":"1969436613","pmid":"https://pubmed.ncbi.nlm.nih.gov/12520061"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkg110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg110","pdf_url":"https://academic.oup.com/nar/article-pdf/31/1/494/7127946/gkg110.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":false,"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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/nar/article-pdf/31/1/494/7127946/gkg110.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070513438","display_name":"Andrea Schafferhans","orcid":"https://orcid.org/0000-0002-5569-6186"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"A. Schafferhans","raw_affiliation_strings":["Lion Bioscience AG, Waldhoferstrasse 98, 69123 Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"Lion Bioscience AG, Waldhoferstrasse 98, 69123 Heidelberg, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5070513438"],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":0.6863,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.66061639,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"31","issue":"1","first_page":"494","last_page":"498"},"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":0.9995999932289124,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9988999962806702,"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-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.8271211385726929},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.6937648057937622},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6653304696083069},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5976518988609314},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5748991966247559},{"id":"https://openalex.org/keywords/sequence-homology","display_name":"Sequence homology","score":0.4772926867008209},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.46661511063575745},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.45930325984954834},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.4564107060432434},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4411046802997589},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42871636152267456},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.4144722521305084},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.36563363671302795},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27688658237457275},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.25138020515441895},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.11715039610862732},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10009875893592834},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06111958622932434}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.8271211385726929},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.6937648057937622},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6653304696083069},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5976518988609314},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5748991966247559},{"id":"https://openalex.org/C2779315201","wikidata":"https://www.wikidata.org/wiki/Q414601","display_name":"Sequence homology","level":4,"score":0.4772926867008209},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.46661511063575745},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.45930325984954834},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.4564107060432434},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4411046802997589},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42871636152267456},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.4144722521305084},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.36563363671302795},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27688658237457275},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.25138020515441895},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.11715039610862732},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10009875893592834},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06111958622932434}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkg110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg110","pdf_url":"https://academic.oup.com/nar/article-pdf/31/1/494/7127946/gkg110.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":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:12520061","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12520061","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:CiteSeerX.psu:10.1.1.602.7973","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.602.7973","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/31/1/494.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:158733","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC165557","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:165557","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/165557","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/gkg110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg110","pdf_url":"https://academic.oup.com/nar/article-pdf/31/1/494/7127946/gkg110.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":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1969436613.pdf","grobid_xml":"https://content.openalex.org/works/W1969436613.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1503558940","https://openalex.org/W1730348256","https://openalex.org/W1994528559","https://openalex.org/W2003144438","https://openalex.org/W2008708467","https://openalex.org/W2009664421","https://openalex.org/W2057029228","https://openalex.org/W2087064593","https://openalex.org/W2099254366","https://openalex.org/W2101220662","https://openalex.org/W2102017976","https://openalex.org/W2130479394","https://openalex.org/W2132045237","https://openalex.org/W2141885858","https://openalex.org/W2153582608","https://openalex.org/W2158714788","https://openalex.org/W2170309361","https://openalex.org/W2628074563","https://openalex.org/W4210531204","https://openalex.org/W4213149192"],"related_works":["https://openalex.org/W2121688928","https://openalex.org/W2103435205","https://openalex.org/W2084743099","https://openalex.org/W2114930488","https://openalex.org/W3132544722","https://openalex.org/W2584773272","https://openalex.org/W3181892255","https://openalex.org/W2099254366","https://openalex.org/W4235583582","https://openalex.org/W2105364679"],"abstract_inverted_index":{"We":[0],"introduce":[1,64],"the":[2,15,48,169],"PSSH":[3,46,121],"('Protein":[4],"Sequence-to-Structure":[5],"Homologies')":[6],"database":[7,22],"derived":[8,67],"from":[9,106],"HSSP2,":[10],"an":[11,166],"improved":[12],"version":[13],"of":[14,20,91,133,137],"HSSP":[16,34],"('Homology-derived":[17],"Secondary":[18],"Structure":[19],"Proteins')":[21],"[Dodge":[23],"et":[24],"al.":[25],"(1998)":[26],"Nucleic":[27],"Acids":[28],"Res.,":[29],"26,":[30],"313-315].":[31],"Whereas":[32],"each":[33,51,72,87],"entry":[35,52,73,88],"lists":[36,74],"all":[37,54,75],"protein":[38,129],"sequences":[39,76],"related":[40,56,77],"to":[41,57,78,104,108,111,168],"a":[42,58,79],"given":[43,59,80],"3D":[44,116],"structure,":[45,109],"is":[47],"'inverse',":[49],"with":[50],"listing":[53],"structures":[55],"sequence.":[60],"In":[61],"addition,":[62],"we":[63],"two":[65],"other":[66],"databases:":[68],"HSSPchain,":[69],"in":[70,85],"which":[71,86],"PDB":[81,97,148],"chain,":[82],"and":[83,110,135,150],"HSSPalign,":[84],"gives":[89,152],"details":[90],"one":[92,96],"sequence":[93,107,113,142],"aligned":[94],"onto":[95,115],"chain.":[98],"This":[99],"re-organization":[100],"makes":[101],"it":[102],"easier":[103],"navigate":[105],"map":[112],"features":[114],"structures.":[117],"Currently":[118],"(September":[119],"2002),":[120],"provides":[122,141],"structural":[123],"information":[124,143],"for":[125,144],"over":[126,145,153],"400":[127],"000":[128,147],"sequences,":[130],"covering":[131],"48%":[132],"SWALL":[134],"61%":[136],"SWISS-PROT":[138],"sequences;":[139],"HSSPchain":[140],"25":[146],"chains,":[149],"HSSPalign":[151],"14":[154],"million":[155],"sequence-to-structure":[156],"alignments.":[157],"The":[158],"databases":[159],"can":[160],"be":[161],"accessed":[162],"via":[163],"SRS":[164,170],"3D,":[165],"extension":[167],"system,":[171],"at":[172],"http://srs3d.ebi.ac.uk/.":[173]},"counts_by_year":[{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}