{"id":"https://openalex.org/W2159275700","doi":"https://doi.org/10.1093/nar/gkr966","title":"PSCDB: a database for protein structural change upon ligand binding","display_name":"PSCDB: a database for protein structural change upon ligand binding","publication_year":2011,"publication_date":"2011-11-10","ids":{"openalex":"https://openalex.org/W2159275700","doi":"https://doi.org/10.1093/nar/gkr966","mag":"2159275700","pmid":"https://pubmed.ncbi.nlm.nih.gov/22080505"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkr966","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr966","pdf_url":null,"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":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":"gold","oa_url":"https://doi.org/10.1093/nar/gkr966","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109644527","display_name":"T. Amemiya","orcid":null},"institutions":[{"id":"https://openalex.org/I60134161","display_name":"Nagoya University","ror":"https://ror.org/04chrp450","country_code":"JP","type":"education","lineage":["https://openalex.org/I60134161"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"T. Amemiya","raw_affiliation_strings":["Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan","Graduate School of Information Science, Nagoya University, Furo-cho, chikusa-ku, Nagoya 464-8601, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan","institution_ids":["https://openalex.org/I60134161"]},{"raw_affiliation_string":"Graduate School of Information Science, Nagoya University, Furo-cho, chikusa-ku, Nagoya 464-8601, Japan","institution_ids":["https://openalex.org/I60134161"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088515417","display_name":"Ryotaro Koike","orcid":"https://orcid.org/0000-0003-2965-6954"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"R. Koike","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021942420","display_name":"Akinori Kidera","orcid":"https://orcid.org/0000-0002-3085-9540"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Kidera","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5004774267","display_name":"Motonori Ota","orcid":"https://orcid.org/0000-0001-9090-668X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Ota","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.4586,"has_fulltext":false,"cited_by_count":49,"citation_normalized_percentile":{"value":0.8151089,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"40","issue":"D1","first_page":"D554","last_page":"D558"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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":0.9994999766349792,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9972000122070312,"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/ligand","display_name":"Ligand (biochemistry)","score":0.6797134876251221},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6301991939544678},{"id":"https://openalex.org/keywords/morphing","display_name":"Morphing","score":0.5254960656166077},{"id":"https://openalex.org/keywords/animation","display_name":"Animation","score":0.5133363604545593},{"id":"https://openalex.org/keywords/motion","display_name":"Motion (physics)","score":0.47906431555747986},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4619038701057434},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.45190751552581787},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.4415537714958191},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.4015038013458252},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32452821731567383},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.23763224482536316},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.23053282499313354},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.1170174777507782},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.11686375737190247},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.10241630673408508},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.07322978973388672}],"concepts":[{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6797134876251221},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6301991939544678},{"id":"https://openalex.org/C50637493","wikidata":"https://www.wikidata.org/wiki/Q1136781","display_name":"Morphing","level":2,"score":0.5254960656166077},{"id":"https://openalex.org/C502989409","wikidata":"https://www.wikidata.org/wiki/Q11425","display_name":"Animation","level":2,"score":0.5133363604545593},{"id":"https://openalex.org/C104114177","wikidata":"https://www.wikidata.org/wiki/Q79782","display_name":"Motion (physics)","level":2,"score":0.47906431555747986},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4619038701057434},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.45190751552581787},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.4415537714958191},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4015038013458252},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32452821731567383},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.23763224482536316},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.23053282499313354},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.1170174777507782},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.11686375737190247},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.10241630673408508},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.07322978973388672},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009038","descriptor_name":"Motion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009038","descriptor_name":"Motion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009038","descriptor_name":"Motion","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":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"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/gkr966","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr966","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:22080505","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22080505","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:pubmedcentral.nih.gov:3245091","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3245091","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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"},{"id":"pmh:oai:open-archive.highwire.org:nar:40/D1/D554","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/40/D1/D554","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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"}],"best_oa_location":{"id":"doi:10.1093/nar/gkr966","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr966","pdf_url":null,"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":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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1963589078","https://openalex.org/W1963819154","https://openalex.org/W1965270719","https://openalex.org/W1966041739","https://openalex.org/W1971248251","https://openalex.org/W1981345243","https://openalex.org/W1987774535","https://openalex.org/W1997486650","https://openalex.org/W1997870466","https://openalex.org/W2010956452","https://openalex.org/W2013640054","https://openalex.org/W2013695178","https://openalex.org/W2025088751","https://openalex.org/W2026418335","https://openalex.org/W2028425871","https://openalex.org/W2043356852","https://openalex.org/W2047953372","https://openalex.org/W2060619005","https://openalex.org/W2066962978","https://openalex.org/W2081492752","https://openalex.org/W2084788321","https://openalex.org/W2091326717","https://openalex.org/W2101766243","https://openalex.org/W2105254477","https://openalex.org/W2122326469","https://openalex.org/W2124483575","https://openalex.org/W2128653811","https://openalex.org/W2140653551","https://openalex.org/W2140889378","https://openalex.org/W2140940323","https://openalex.org/W2142270082","https://openalex.org/W2152257846","https://openalex.org/W2154715418","https://openalex.org/W2158714788","https://openalex.org/W2161870238","https://openalex.org/W2170441710","https://openalex.org/W2171371127"],"related_works":["https://openalex.org/W3008660221","https://openalex.org/W200966836","https://openalex.org/W1564870812","https://openalex.org/W2367722113","https://openalex.org/W2041694917","https://openalex.org/W4386436297","https://openalex.org/W46965012","https://openalex.org/W3095637956","https://openalex.org/W2167420772","https://openalex.org/W2133070552"],"abstract_inverted_index":{"Proteins":[0],"are":[1],"flexible":[2],"molecules":[3],"that":[4],"undergo":[5],"structural":[6,38,48,87,99,151],"changes":[7,39,88],"to":[8,41],"function.":[9],"The":[10],"Protein":[11,63],"Data":[12],"Bank":[13],"contains":[14],"multiple":[15],"entries":[16],"for":[17,35],"identical":[18],"proteins":[19],"determined":[20],"under":[21],"different":[22],"conditions,":[23],"e.g.":[24],"with":[25,79],"and":[26,52,60,121],"without":[27],"a":[28,83,146],"ligand":[29,80,114],"molecule,":[30],"which":[31],"provides":[32,127],"important":[33],"information":[34,140],"understanding":[36],"the":[37,62,69,75,85,142,150],"related":[40],"protein":[42,47,86],"functions.":[43],"We":[44],"gathered":[45],"839":[46],"pairs":[49],"of":[50,129,149],"ligand-free":[51],"ligand-bound":[53],"states":[54],"from":[55],"monomeric":[56],"or":[57],"homo-dimeric":[58],"proteins,":[59],"constructed":[61],"Structural":[64],"Change":[65],"DataBase":[66],"(PSCDB).":[67],"In":[68],"database,":[70],"we":[71],"focused":[72],"on":[73],"whether":[74],"motions":[76],"were":[77,89],"coupled":[78,95,105],"binding.":[81],"As":[82],"result,":[84],"classified":[90],"into":[91],"seven":[92],"classes,":[93],"i.e.":[94],"domain":[96,102],"motion":[97,103,107,111,115,119,124],"(59":[98],"changes),":[100],"independent":[101,109],"(70),":[104],"local":[106,110],"(125),":[108],"(135),":[112],"burying":[113],"(104),":[116],"no":[117],"significant":[118],"(311)":[120],"other":[122],"type":[123],"(35).":[125],"PSCDB":[126,153],"lists":[128],"each":[130,133],"class.":[131],"On":[132],"entry":[134],"page,":[135],"users":[136],"can":[137],"view":[138],"detailed":[139],"about":[141],"motion,":[143],"accompanied":[144],"by":[145],"morphing":[147],"animation":[148],"changes.":[152],"is":[154],"available":[155],"at":[156],"http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/.":[157]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
