{"id":"https://openalex.org/W2078247418","doi":"https://doi.org/10.1093/nar/gkn326","title":"Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure","display_name":"Domain Hierarchy and closed Loops (DHcL): a server for exploring hierarchy of protein domain structure","publication_year":2008,"publication_date":"2008-05-23","ids":{"openalex":"https://openalex.org/W2078247418","doi":"https://doi.org/10.1093/nar/gkn326","mag":"2078247418","pmid":"https://pubmed.ncbi.nlm.nih.gov/18502776"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkn326","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn326","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W239/18782350/gkn326.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/36/suppl_2/W239/18782350/gkn326.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014999137","display_name":"Grzegorz Koczyk","orcid":"https://orcid.org/0000-0002-5414-4689"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Grzegorz Koczyk","raw_affiliation_strings":["Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen 5008, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen 5008, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033504184","display_name":"Igor N. Berezovsky","orcid":"https://orcid.org/0000-0002-3315-8483"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Igor N. Berezovsky","raw_affiliation_strings":["Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen 5008, Norway and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen 5008, Norway and","institution_ids":["https://openalex.org/I4432739"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4432739"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":0.8424,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.72877315,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"36","issue":"suppl_2","first_page":"W239","last_page":"W245"},"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":0.9994999766349792,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9743000268936157,"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/hierarchy","display_name":"Hierarchy","score":0.8200573921203613},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5870271921157837},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5502703785896301},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5260943174362183},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.5169731974601746},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.514537513256073},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.48642945289611816},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48545747995376587},{"id":"https://openalex.org/keywords/van-der-waals-force","display_name":"van der Waals force","score":0.41350215673446655},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.370846688747406},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3623011112213135},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33453869819641113},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.30129939317703247},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.19415688514709473},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.17488741874694824},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.16797569394111633},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.16477277874946594},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12935417890548706}],"concepts":[{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.8200573921203613},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5870271921157837},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5502703785896301},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5260943174362183},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.5169731974601746},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.514537513256073},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.48642945289611816},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48545747995376587},{"id":"https://openalex.org/C126061179","wikidata":"https://www.wikidata.org/wiki/Q189627","display_name":"van der Waals force","level":3,"score":0.41350215673446655},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.370846688747406},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3623011112213135},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33453869819641113},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30129939317703247},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.19415688514709473},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.17488741874694824},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.16797569394111633},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.16477277874946594},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12935417890548706},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","level":1,"score":0.0},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":"D008958","descriptor_name":"Models, Molecular","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":"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":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkn326","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn326","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W239/18782350/gkn326.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:18502776","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18502776","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:2447749","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2447749","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/gkn326","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn326","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W239/18782350/gkn326.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":[{"id":"https://metadata.un.org/sdg/7","score":0.49000000953674316,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320323299","display_name":"Norges Forskningsr\u00e5d","ror":"https://ror.org/00epmv149"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2078247418.pdf","grobid_xml":"https://content.openalex.org/works/W2078247418.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1786523947","https://openalex.org/W1965266514","https://openalex.org/W1990896235","https://openalex.org/W2003996804","https://openalex.org/W2011574913","https://openalex.org/W2034477756","https://openalex.org/W2049355199","https://openalex.org/W2085277871","https://openalex.org/W2106320506","https://openalex.org/W2108067237","https://openalex.org/W2108541140","https://openalex.org/W2111374837","https://openalex.org/W2113403117","https://openalex.org/W2138116388","https://openalex.org/W2156611610","https://openalex.org/W2168172687","https://openalex.org/W4242952474"],"related_works":["https://openalex.org/W2090630809","https://openalex.org/W2153650863","https://openalex.org/W4246050813","https://openalex.org/W4253991465","https://openalex.org/W2298319713","https://openalex.org/W3207853523","https://openalex.org/W2013211627","https://openalex.org/W2032140021","https://openalex.org/W3038491195","https://openalex.org/W2069319199"],"abstract_inverted_index":{"Domain":[0],"hierarchy":[1,14],"and":[2,19,34,63,105,120],"closed":[3,32,99,118],"loops":[4,33],"(DHcL)":[5],"(http://sitron.bccs.uib.no/dhcl/)":[6],"is":[7,133],"a":[8,41,53,71,76,81,112],"web":[9],"server":[10,29,110,132],"that":[11],"delineates":[12],"energy":[13],"of":[15,25,60,86,92,97,116],"protein":[16,46,61,78],"domain":[17,47,66],"structure":[18,79],"detects":[20],"domains":[21,93],"at":[22,94],"different":[23,95],"levels":[24,96],"this":[26],"hierarchy.":[27,48],"The":[28,49,68,84,109],"also":[30],"identifies":[31],"van":[35,101,121],"der":[36,102,122],"Waals":[37,103,123],"locks,":[38],"which":[39],"constitute":[40],"structural":[42],"basis":[43],"for":[44,56,125],"the":[45,87,90],"DHcL":[50,131],"can":[51],"be":[52],"useful":[54],"tool":[55],"an":[57],"express":[58],"analysis":[59,88],"structures":[62,128],"their":[64,106],"alternative":[65],"decompositions.":[67],"user":[69],"submits":[70],"PDB":[72,82],"identifier(s)":[73],"or":[74],"uploads":[75],"3D":[77],"in":[80,129],"format.":[83],"results":[85],"are":[89],"location":[91],"hierarchy,":[98],"loops,":[100],"locks":[104,124],"interactive":[107],"visualization.":[108],"maintains":[111],"regularly":[113],"updated":[114],"database":[115],"domains,":[117],"loop":[119],"all":[126],"X-ray":[127],"PDB.":[130],"available":[134],"at:":[135],"http://sitron.bccs.uib.no/dhcl.":[136]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}
