{"id":"https://openalex.org/W2127489230","doi":"https://doi.org/10.1093/nar/gkt1189","title":"ArchDB 2014: structural classification of loops in proteins","display_name":"ArchDB 2014: structural classification of loops in proteins","publication_year":2013,"publication_date":"2013-11-21","ids":{"openalex":"https://openalex.org/W2127489230","doi":"https://doi.org/10.1093/nar/gkt1189","mag":"2127489230","pmid":"https://pubmed.ncbi.nlm.nih.gov/24265221"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkt1189","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt1189","pdf_url":"https://academic.oup.com/nar/article-pdf/42/D1/D315/16802150/gkt1189.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","license_id":"https://openalex.org/licenses/cc-by","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/42/D1/D315/16802150/gkt1189.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048998113","display_name":"Jaume Bonet","orcid":"https://orcid.org/0000-0001-5210-4387"},"institutions":[{"id":"https://openalex.org/I16038530","display_name":"Aberystwyth University","ror":"https://ror.org/015m2p889","country_code":"GB","type":"education","lineage":["https://openalex.org/I16038530"]},{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]},{"id":"https://openalex.org/I4210146599","display_name":"Institute of Biological, Environmental and Rural Sciences","ror":"https://ror.org/051wgfj58","country_code":"GB","type":"education","lineage":["https://openalex.org/I16038530","https://openalex.org/I2799693246","https://openalex.org/I4210087105","https://openalex.org/I4210146599"]}],"countries":["ES","GB"],"is_corresponding":false,"raw_author_name":"Jaume Bonet","raw_affiliation_strings":["Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB), Barcelona, Catalonia, 08950, Spain and Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA Aberystwyth, Ceredigion, UK","Pompeu Fabra University, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Structural Bioinformatics Lab (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Research Park of Biomedicine (PRBB), Barcelona, Catalonia, 08950, Spain and Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA Aberystwyth, Ceredigion, UK","institution_ids":["https://openalex.org/I2801864671","https://openalex.org/I4210146599","https://openalex.org/I16038530"]},{"raw_affiliation_string":"Pompeu Fabra University, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081228191","display_name":"Joan Planas-Iglesias","orcid":"https://orcid.org/0000-0002-6279-2483"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Joan Planas-Iglesias","raw_affiliation_strings":["Pompeu Fabra University, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pompeu Fabra University, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038679061","display_name":"Javier Garc\u0131\u0301a-Garc\u0131\u0301a","orcid":"https://orcid.org/0000-0001-9539-2606"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Javier Garcia-Garcia","raw_affiliation_strings":["Pompeu Fabra University, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pompeu Fabra University, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031156142","display_name":"Manuel Alejandro Mar\u00edn-L\u00f3pez","orcid":"https://orcid.org/0000-0003-0833-3574"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Manuel A. Mar\u00edn-L\u00f3pez","raw_affiliation_strings":["Pompeu Fabra University, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pompeu Fabra University, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090989775","display_name":"Narc\u00eds Fern\u00e1ndez\u2010Fuentes","orcid":"https://orcid.org/0000-0002-6421-1080"},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Narcis Fernandez-Fuentes","raw_affiliation_strings":["Pompeu Fabra University, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pompeu Fabra University, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111840557","display_name":"Baldo Oliva","orcid":null},"institutions":[{"id":"https://openalex.org/I170486558","display_name":"Universitat Pompeu Fabra","ror":"https://ror.org/04n0g0b29","country_code":"ES","type":"education","lineage":["https://openalex.org/I170486558"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Baldo Oliva","raw_affiliation_strings":["Pompeu Fabra University, Barcelona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pompeu Fabra University, Barcelona, Spain","institution_ids":["https://openalex.org/I170486558"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"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":2.8427,"has_fulltext":false,"cited_by_count":49,"citation_normalized_percentile":{"value":0.91140471,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"42","issue":"D1","first_page":"D315","last_page":"D319"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","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"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9965999722480774,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.9929999709129333,"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/biology","display_name":"Biology","score":0.9303612112998962},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5787978768348694},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3638274669647217},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3401736617088318}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9303612112998962},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5787978768348694},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3638274669647217},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3401736617088318}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkt1189","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt1189","pdf_url":"https://academic.oup.com/nar/article-pdf/42/D1/D315/16802150/gkt1189.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:24265221","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24265221","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:europepmc.org:2943096","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3964960","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:repositori-api.upf.edu:10230/23221","is_oa":true,"landing_page_url":"http://hdl.handle.net/10230/23221","pdf_url":null,"source":{"id":"https://openalex.org/S4306402615","display_name":"Repositori digital de la UPF (Universitat Pompeu Fabra)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I170486558","host_organization_name":"Universitat Pompeu Fabra","host_organization_lineage":["https://openalex.org/I170486558"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:aber.ac.uk:publications/e83ee58f-6f89-4a40-ae3e-e4b63298018d","is_oa":false,"landing_page_url":"http://www.scopus.com/inward/record.url?scp=84891774264&partnerID=8YFLogxK","pdf_url":null,"source":{"id":"https://openalex.org/S4306401660","display_name":"Aberystwyth Research portal (Aberystwyth University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I16038530","host_organization_name":"Aberystwyth University","host_organization_lineage":["https://openalex.org/I16038530"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""}],"best_oa_location":{"id":"doi:10.1093/nar/gkt1189","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt1189","pdf_url":"https://academic.oup.com/nar/article-pdf/42/D1/D315/16802150/gkt1189.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8892534858","display_name":null,"funder_award_id":"BBS/E/W/10962A01D","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2127489230.pdf"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1806630989","https://openalex.org/W1871470604","https://openalex.org/W1967686998","https://openalex.org/W1969425147","https://openalex.org/W1973695911","https://openalex.org/W1975449945","https://openalex.org/W1985744441","https://openalex.org/W2002850151","https://openalex.org/W2004234681","https://openalex.org/W2005240848","https://openalex.org/W2008708467","https://openalex.org/W2020960844","https://openalex.org/W2032643862","https://openalex.org/W2048947602","https://openalex.org/W2049870911","https://openalex.org/W2050085817","https://openalex.org/W2080022084","https://openalex.org/W2082535576","https://openalex.org/W2084367350","https://openalex.org/W2085144661","https://openalex.org/W2085162946","https://openalex.org/W2085697834","https://openalex.org/W2094203741","https://openalex.org/W2100981947","https://openalex.org/W2101333065","https://openalex.org/W2111973517","https://openalex.org/W2123742794","https://openalex.org/W2125725297","https://openalex.org/W2130479394","https://openalex.org/W2137052779","https://openalex.org/W2137760272","https://openalex.org/W2164479678","https://openalex.org/W2170747616","https://openalex.org/W2612166593"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1971568933","https://openalex.org/W2013243191","https://openalex.org/W2117258802"],"abstract_inverted_index":{"The":[0,152,173],"function":[1,70,111],"of":[2,41,47,55,58,71,77,86,150,155,176],"a":[3,37,59,65,72,124,144,158,166],"protein":[4,73,78,87,99,102],"is":[5,12,89],"determined":[6],"by":[7,14],"its":[8],"three-dimensional":[9],"structure,":[10],"which":[11],"formed":[13],"regular":[15,29],"(i.e.":[16],"\u03b2-strands":[17],"and":[18,20,49,74,80,107,110,126,147,161,165,184],"\u03b1-helices)":[19],"non-periodic":[21],"structural":[22,30,84],"units":[23,35],"such":[24,123],"as":[25],"loops.":[26],"Compared":[27],"to":[28],"elements,":[31],"non-periodic,":[32],"non-repetitive":[33],"conformational":[34],"enclose":[36],"much":[38],"higher":[39],"degree":[40],"variability--raising":[42],"difficulties":[43],"in":[44,68,96,181],"the":[45,56,69,83,114,133,137],"identification":[46],"regularities,":[48],"yet":[50],"represent":[51],"an":[52,90,129],"important":[53,91,130],"part":[54],"structure":[57,100],"protein.":[60],"Indeed,":[61],"loops":[62,88,180],"often":[63],"play":[64],"pivotal":[66],"role":[67],"different":[75],"aspects":[76],"folding":[79],"dynamics.":[81],"Therefore,":[82],"classification":[85],"subject":[92],"with":[93],"clear":[94],"applications":[95],"homology":[97],"modelling,":[98],"prediction,":[101],"design":[103,106],"(e.g.":[104],"enzyme":[105],"catalytic":[108],"loops)":[109],"prediction.":[112],"ArchDB,":[113],"database":[115],"presented":[116],"here":[117],"(freely":[118],"available":[119],"at":[120],"http://sbi.imim.es/archdb),":[121],"represents":[122],"resource":[125],"has":[127],"been":[128],"asset":[131],"for":[132],"scientific":[134],"community":[135],"throughout":[136],"years.":[138],"In":[139],"this":[140],"article,":[141],"we":[142],"present":[143],"completely":[145],"reworked":[146],"updated":[148],"version":[149,154,175],"ArchDB.":[151],"new":[153],"ArchDB":[156,177],"features":[157],"novel,":[159],"fast":[160],"user-friendly":[162],"web-based":[163],"interface,":[164],"novel":[167],"graph-based,":[168],"computationally":[169],"efficient,":[170],"clustering":[171],"algorithm.":[172],"current":[174],"classifies":[178],"149,134":[179],"5739":[182],"classes":[183],"9608":[185],"subclasses.":[186]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":6}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
