{"id":"https://openalex.org/W2143695538","doi":"https://doi.org/10.1093/nar/gkq489","title":"deconSTRUCT: general purpose protein database search on the substructure level","display_name":"deconSTRUCT: general purpose protein database search on the substructure level","publication_year":2010,"publication_date":"2010-06-03","ids":{"openalex":"https://openalex.org/W2143695538","doi":"https://doi.org/10.1093/nar/gkq489","mag":"2143695538","pmid":"https://pubmed.ncbi.nlm.nih.gov/20522512"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkq489","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq489","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W590/16774264/gkq489.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/38/suppl_2/W590/16774264/gkq489.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040511420","display_name":"Zong Hong Zhang","orcid":"https://orcid.org/0000-0002-8056-891X"},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Zong Hong Zhang","raw_affiliation_strings":["Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix, Singapore","institution_ids":["https://openalex.org/I4210148498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060401499","display_name":"Kavitha Bharatham","orcid":"https://orcid.org/0000-0002-2610-7768"},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Kavitha Bharatham","raw_affiliation_strings":["Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix, Singapore 138671"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix, Singapore 138671","institution_ids":["https://openalex.org/I4210148498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057277568","display_name":"Westley Sherman","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Westley A. Sherman","raw_affiliation_strings":["Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix, Singapore 138671"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix, Singapore 138671","institution_ids":["https://openalex.org/I4210148498"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028294634","display_name":"Ivana Mihalek","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Ivana Mihalek","raw_affiliation_strings":["Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix, Singapore 138671"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute 30 Biopolis Street, #07-01 Matrix, Singapore 138671","institution_ids":["https://openalex.org/I4210148498"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5028294634"],"corresponding_institution_ids":["https://openalex.org/I4210148498"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.8055,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.72218802,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"38","issue":"suppl_2","first_page":"W590","last_page":"W594"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9983999729156494,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9983000159263611,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6207543015480042},{"id":"https://openalex.org/keywords/hash-function","display_name":"Hash function","score":0.5595892667770386},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5417232513427734},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5280880331993103},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4942021667957306},{"id":"https://openalex.org/keywords/usable","display_name":"USable","score":0.43577560782432556},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.382360577583313},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3612593710422516},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3225245475769043},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2183300256729126},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21197989583015442},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.18938854336738586}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6207543015480042},{"id":"https://openalex.org/C99138194","wikidata":"https://www.wikidata.org/wiki/Q183427","display_name":"Hash function","level":2,"score":0.5595892667770386},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5417232513427734},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5280880331993103},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4942021667957306},{"id":"https://openalex.org/C2780615836","wikidata":"https://www.wikidata.org/wiki/Q2471869","display_name":"USable","level":2,"score":0.43577560782432556},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.382360577583313},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3612593710422516},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3225245475769043},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2183300256729126},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21197989583015442},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.18938854336738586}],"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":"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":"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":"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":"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":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkq489","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq489","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W590/16774264/gkq489.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:20522512","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20522512","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:10.1.1.354.4610","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.354.4610","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/97/6c/Nucleic_Acids_Res_2010_Jul_1_38(Web_Server_issue)_W590-W594.tar.gz","raw_type":"text"},{"id":"pmh:oai:espace.library.uq.edu.au:UQ:c254e80","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306402388","display_name":"Queensland's institutional digital repository (The University of Queensland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165143802","host_organization_name":"The University of Queensland","host_organization_lineage":["https://openalex.org/I165143802"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:open-archive.highwire.org:nar:38/suppl_2/W590","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/38/suppl_2/W590","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:2896154","is_oa":true,"landing_page_url":"http://doi.org/10.1093/nar/gkq489","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"}],"best_oa_location":{"id":"doi:10.1093/nar/gkq489","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq489","pdf_url":"https://academic.oup.com/nar/article-pdf/38/suppl_2/W590/16774264/gkq489.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5199999809265137,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320696","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09"},{"id":"https://openalex.org/F4320335846","display_name":"Biomedical Research Council","ror":"https://ror.org/03xy0wx88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2143695538.pdf","grobid_xml":"https://content.openalex.org/works/W2143695538.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W42096393","https://openalex.org/W255996521","https://openalex.org/W1510161841","https://openalex.org/W1801992990","https://openalex.org/W1984349320","https://openalex.org/W1996945721","https://openalex.org/W2017727500","https://openalex.org/W2027337253","https://openalex.org/W2050330741","https://openalex.org/W2058983001","https://openalex.org/W2061827467","https://openalex.org/W2062318714","https://openalex.org/W2081771568","https://openalex.org/W2097311600","https://openalex.org/W2097642323","https://openalex.org/W2098125835","https://openalex.org/W2102245393","https://openalex.org/W2108067237","https://openalex.org/W2108138353","https://openalex.org/W2113563422","https://openalex.org/W2125062378","https://openalex.org/W2126016150","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2133225033","https://openalex.org/W2137955461","https://openalex.org/W2141920771","https://openalex.org/W2142749069","https://openalex.org/W2144998676","https://openalex.org/W2148101168","https://openalex.org/W2151785844","https://openalex.org/W2152326664","https://openalex.org/W2158309235","https://openalex.org/W6601702993","https://openalex.org/W6609701964"],"related_works":["https://openalex.org/W2982321410","https://openalex.org/W95465806","https://openalex.org/W2392004567","https://openalex.org/W2940029036","https://openalex.org/W2756595502","https://openalex.org/W2010789764","https://openalex.org/W2219281195","https://openalex.org/W2187233292","https://openalex.org/W2532162280","https://openalex.org/W82655570"],"abstract_inverted_index":{"deconSTRUCT":[0,67],"webserver":[1],"offers":[2],"an":[3],"interface":[4],"to":[5,37,68,116],"a":[6,13,42,96,99,102,146],"protein":[7,19,64],"database":[8],"search":[9,77],"engine,":[10],"usable":[11],"for":[12,130],"general":[14],"purpose":[15],"detection":[16],"of":[17,45,53,60,74,81,95,107,120,123,133,139],"similar":[18],"(sub)structures.":[20],"Initially,":[21],"it":[22],"deconstructs":[23],"the":[24,35,38,48,61,70,75,89,93,105,108,117,121,124,127,134],"query":[25],"structure":[26,30,65],"into":[27],"its":[28],"secondary":[29],"elements":[31],"(SSEs)":[32],"and":[33,50,57,72,136,143],"reassembles":[34],"match":[36,103],"target":[39],"by":[40],"requiring":[41],"(tunable)":[43],"degree":[44],"similarity":[46],"in":[47,92],"direction":[49],"sequential":[51],"order":[52],"SSEs.":[54],"Hierarchical":[55],"organization":[56],"judicious":[58],"use":[59],"information":[62,91],"about":[63],"enables":[66],"achieve":[69],"sensitivity":[71],"specificity":[73],"established":[76],"engines":[78],"at":[79,153],"orders":[80],"magnitude":[82],"increased":[83],"speed,":[84],"without":[85],"tying":[86],"up":[87],"irretrievably":[88],"substructure":[90],"form":[94],"hash.":[97],"In":[98],"post-processing":[100],"step,":[101],"on":[104],"level":[106],"backbone":[109],"atoms":[110],"is":[111,151],"constructed.":[112],"The":[113,149],"results":[114],"presented":[115],"user":[118],"consist":[119],"list":[122],"matched":[125],"SSEs,":[126],"transformation":[128],"matrix":[129],"rigid":[131],"superposition":[132],"structures":[135],"several":[137],"ways":[138],"visualization,":[140],"both":[141],"downloadable":[142],"implemented":[144],"as":[145],"web-browser":[147],"plug-in.":[148],"server":[150],"available":[152],"http://epsf.bmad.bii.a-star.edu.sg/struct_server.html.":[154]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
