{"id":"https://openalex.org/W2051872583","doi":"https://doi.org/10.1093/nar/gki402","title":"PISCES: recent improvements to a PDB sequence culling server","display_name":"PISCES: recent improvements to a PDB sequence culling server","publication_year":2005,"publication_date":"2005-06-26","ids":{"openalex":"https://openalex.org/W2051872583","doi":"https://doi.org/10.1093/nar/gki402","mag":"2051872583","pmid":"https://pubmed.ncbi.nlm.nih.gov/15980589"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki402","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W94/7622855/gki402.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/33/suppl_2/W94/7622855/gki402.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081855187","display_name":"Guiquan Wang","orcid":"https://orcid.org/0000-0003-4753-7676"},"institutions":[{"id":"https://openalex.org/I1289437631","display_name":"Fox Chase Cancer Center","ror":"https://ror.org/0567t7073","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1289437631","https://openalex.org/I4210122924"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"G. Wang","raw_affiliation_strings":["Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA","Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia PA 19111 USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA","institution_ids":["https://openalex.org/I1289437631"]},{"raw_affiliation_string":"Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia PA 19111 USA#TAB#","institution_ids":["https://openalex.org/I1289437631"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053977807","display_name":"Roland L. Dunbrack","orcid":"https://orcid.org/0000-0001-7674-6667"},"institutions":[{"id":"https://openalex.org/I1289437631","display_name":"Fox Chase Cancer Center","ror":"https://ror.org/0567t7073","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1289437631","https://openalex.org/I4210122924"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. L. Dunbrack","raw_affiliation_strings":["Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia, PA 19111, USA","Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia PA 19111 USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia, PA 19111, USA","institution_ids":["https://openalex.org/I1289437631"]},{"raw_affiliation_string":"Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia PA 19111 USA#TAB#","institution_ids":["https://openalex.org/I1289437631"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5081855187"],"corresponding_institution_ids":["https://openalex.org/I1289437631"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.7494,"has_fulltext":true,"cited_by_count":371,"citation_normalized_percentile":{"value":0.9585949,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"33","issue":"Web Server","first_page":"W94","last_page":"W98"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987999796867371,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9958000183105469,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.8058419227600098},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6144226789474487},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.594534695148468},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.5457444190979004},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.4726085960865021},{"id":"https://openalex.org/keywords/culling","display_name":"Culling","score":0.453476220369339},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.42042437195777893},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4166545569896698},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3226006031036377},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15564662218093872},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11958542466163635},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.11085182428359985},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.08383041620254517}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.8058419227600098},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6144226789474487},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.594534695148468},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.5457444190979004},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.4726085960865021},{"id":"https://openalex.org/C52991690","wikidata":"https://www.wikidata.org/wiki/Q1740042","display_name":"Culling","level":3,"score":0.453476220369339},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.42042437195777893},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4166545569896698},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3226006031036377},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15564662218093872},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11958542466163635},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.11085182428359985},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08383041620254517},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C194775826","wikidata":"https://www.wikidata.org/wiki/Q209542","display_name":"Herd","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","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":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}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gki402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki402","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W94/7622855/gki402.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15980589","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15980589","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:10.1.1.83.7130","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.83.7130","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://dunbrack.fccc.edu/Guoli/pisces.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:1783464","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1160163","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gki402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki402","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W94/7622855/gki402.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.699999988079071,"id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G1064781665","display_name":null,"funder_award_id":"CA06972","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G8748870931","display_name":null,"funder_award_id":"R01 HG002302","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G927486529","display_name":null,"funder_award_id":"R01-HG02302","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2051872583.pdf","grobid_xml":"https://content.openalex.org/works/W2051872583.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1992426410","https://openalex.org/W2062693912","https://openalex.org/W2088933990","https://openalex.org/W2096525273","https://openalex.org/W2099235960","https://openalex.org/W2106882534","https://openalex.org/W2116449290","https://openalex.org/W2130479394","https://openalex.org/W2133657429","https://openalex.org/W2137154596","https://openalex.org/W2137995988","https://openalex.org/W2147809382","https://openalex.org/W2149758239","https://openalex.org/W2150556577","https://openalex.org/W2152326664","https://openalex.org/W2153153865","https://openalex.org/W2158714788","https://openalex.org/W2168211076","https://openalex.org/W2168267323","https://openalex.org/W4242739003"],"related_works":["https://openalex.org/W4232154957","https://openalex.org/W4292058683","https://openalex.org/W4307362031","https://openalex.org/W4389222350","https://openalex.org/W4376646754","https://openalex.org/W2022209941","https://openalex.org/W4205671017","https://openalex.org/W4375844720","https://openalex.org/W3132544722","https://openalex.org/W3181892255"],"abstract_inverted_index":{"PISCES":[0,57,85,139,191],"is":[1,34,219],"a":[2,17,60,88,107,117,121,153,176,194],"database":[3],"server":[4,58,151,192,218],"for":[5,183,208],"producing":[6],"lists":[7],"of":[8,19,41,62,160,202],"sequences":[9,144],"from":[10,175],"the":[11,32,37,42,48,92,98,132,135,179,184,190,198,203],"Protein":[12],"Data":[13],"Bank":[14],"(PDB)":[15],"using":[16],"number":[18],"entry-":[20],"and":[21,24,51,64,77,148],"chain-specific":[22],"criteria":[23],"mutual":[25],"sequence":[26,49,69,81,122,136,209],"identity.":[27],"Our":[28],"goal":[29],"in":[30,95,127,131],"culling":[31,100],"PDB":[33,93,185,204],"to":[35,67,90,97,124,155],"provide":[36],"longest":[38],"list":[39,108,133,159],"possible":[40],"highest":[43],"resolution":[44],"structures":[45],"that":[46,113,119,165],"fulfill":[47],"identity":[50,123,137],"structural":[52],"quality":[53],"cut-offs.":[54],"The":[55,150,211,217],"new":[56],"uses":[59],"combination":[61],"PSI-BLAST":[63],"structure-based":[65],"alignments":[66,76],"determine":[68],"identities.":[70],"Structure":[71],"alignment":[72],"produces":[73],"more":[74,79],"complete":[75],"therefore":[78],"accurate":[80],"identities":[82],"than":[83],"PSI-BLAST.":[84],"now":[86],"allows":[87,152],"user":[89,154],"cull":[91,156],"by-entry":[94],"addition":[96],"standard":[99],"by":[101,193],"individual":[102],"chains.":[103],"In":[104],"this":[105],"scenario,":[106],"will":[109],"contain":[110],"only":[111],"entries":[112,161],"do":[114],"not":[115],"have":[116],"chain":[118,126],"has":[120],"any":[125,128],"other":[129,166],"entry":[130],"over":[134],"cut-off.":[138],"also":[140],"provides":[141],"fully":[142],"annotated":[143],"including":[145],"gene":[146],"name":[147],"species.":[149],"an":[157],"input":[158],"or":[162],"chains,":[163],"so":[164],"criteria,":[167],"such":[168],"as":[169],"function,":[170],"can":[171,186],"be":[172,187],"used.":[173],"Results":[174],"search":[177],"on":[178],"re-engineered":[180],"RCSB's":[181],"site":[182],"entered":[188],"into":[189],"single":[195],"click,":[196],"combining":[197],"powerful":[199],"searching":[200],"abilities":[201],"with":[205],"PISCES's":[206],"utilities":[207],"culling.":[210],"server's":[212],"data":[213],"are":[214],"updated":[215],"weekly.":[216],"available":[220],"at":[221],"http://dunbrack.fccc.edu/pisces.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":18},{"year":2022,"cited_by_count":28},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":15},{"year":2018,"cited_by_count":24},{"year":2017,"cited_by_count":19},{"year":2016,"cited_by_count":17},{"year":2015,"cited_by_count":34},{"year":2014,"cited_by_count":24},{"year":2013,"cited_by_count":35},{"year":2012,"cited_by_count":19}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
