{"id":"https://openalex.org/W2137955461","doi":"https://doi.org/10.1093/bioinformatics/btn507","title":"Searching protein structure databases with DaliLite v.3","display_name":"Searching protein structure databases with DaliLite v.3","publication_year":2008,"publication_date":"2008-09-25","ids":{"openalex":"https://openalex.org/W2137955461","doi":"https://doi.org/10.1093/bioinformatics/btn507","mag":"2137955461","pmid":"https://pubmed.ncbi.nlm.nih.gov/18818215"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn507","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn507","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/23/2780/49055584/bioinformatics_24_23_2780.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/23/2780/49055584/bioinformatics_24_23_2780.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064498279","display_name":"Liisa Holm","orcid":"https://orcid.org/0000-0002-7807-2966"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"L. Holm","raw_affiliation_strings":["1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089625847","display_name":"Sakari K\u00e4\u00e4ri\u00e4inen","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"S. K\u00e4\u00e4ri\u00e4inen","raw_affiliation_strings":["1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079173957","display_name":"P\u00e4ivi Rosenstr\u00f6m","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"P. Rosenstr\u00f6m","raw_affiliation_strings":["1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039357882","display_name":"Alain Schenkel","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"A. Schenkel","raw_affiliation_strings":["1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biological and Environmental Sciences, and 2Institute of Biotechnology, P.O.Box 56 (Viikinkaari 5), 00014 University of Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5064498279"],"corresponding_institution_ids":["https://openalex.org/I133731052"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":64.8353,"has_fulltext":true,"cited_by_count":1038,"citation_normalized_percentile":{"value":0.99971972,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"24","issue":"23","first_page":"2780","last_page":"2781"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.33250001072883606,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.33250001072883606,"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":0.1923999935388565,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.17820000648498535,"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/computer-science","display_name":"Computer science","score":0.7575714588165283},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5693303346633911},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5619109869003296},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.5124593377113342},{"id":"https://openalex.org/keywords/pruning","display_name":"Pruning","score":0.4883382022380829},{"id":"https://openalex.org/keywords/server","display_name":"Server","score":0.4801004230976105},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.4676347076892853},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.45475709438323975},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4271661341190338},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.41975271701812744},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.2875206172466278},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.2061181366443634},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.0825175940990448}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7575714588165283},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5693303346633911},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5619109869003296},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.5124593377113342},{"id":"https://openalex.org/C108010975","wikidata":"https://www.wikidata.org/wiki/Q500094","display_name":"Pruning","level":2,"score":0.4883382022380829},{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.4801004230976105},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.4676347076892853},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.45475709438323975},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4271661341190338},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.41975271701812744},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2875206172466278},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.2061181366443634},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0825175940990448},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C6557445","wikidata":"https://www.wikidata.org/wiki/Q173113","display_name":"Agronomy","level":1,"score":0.0}],"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","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":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/bioinformatics/btn507","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn507","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/23/2780/49055584/bioinformatics_24_23_2780.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18818215","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18818215","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:1399460","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC2639270","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:2639270","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2639270","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btn507","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn507","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/23/2780/49055584/bioinformatics_24_23_2780.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2137955461.pdf","grobid_xml":"https://content.openalex.org/works/W2137955461.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1972718882","https://openalex.org/W2085277871","https://openalex.org/W2096943217","https://openalex.org/W2110397834","https://openalex.org/W2144998676","https://openalex.org/W2156125289","https://openalex.org/W2161056921","https://openalex.org/W6681619517"],"related_works":["https://openalex.org/W2020669016","https://openalex.org/W2088162897","https://openalex.org/W2090630809","https://openalex.org/W4387804157","https://openalex.org/W2106612397","https://openalex.org/W2518314460","https://openalex.org/W2401430279","https://openalex.org/W2013211627","https://openalex.org/W2069319199","https://openalex.org/W2032140021"],"abstract_inverted_index":{"UNLABELLED:":[0],"The":[1,59,95,158,172],"Red":[2],"Queen":[3],"said,":[4],"'It":[5],"takes":[6],"all":[7],"the":[8,16,33,88,102,116,122,134],"running":[9,169],"you":[10],"can":[11,174],"do,":[12],"to":[13,65,74,100,120],"keep":[14],"in":[15,32,77,87,92,115,138],"same":[17],"place.'":[18],"Lewis":[19],"Carrol":[20],"MOTIVATION:":[21],"Newly":[22],"solved":[23],"protein":[24,162],"structures":[25,30,46,63,86,137],"are":[26,53,72,83],"routinely":[27],"scanned":[28],"against":[29],"already":[31],"Protein":[34],"Data":[35],"Bank":[36],"(PDB)":[37],"using":[38,130],"Internet":[39],"servers.":[40],"In":[41],"favourable":[42],"cases,":[43],"comparing":[44,57],"3D":[45],"may":[47],"reveal":[48],"biologically":[49],"interesting":[50],"similarities":[51],"that":[52,146],"not":[54],"detectable":[55],"by":[56,126],"sequences.":[58],"number":[60],"of":[61,136],"known":[62],"continues":[64],"grow":[66],"exponentially.":[67],"Sensitive-thorough":[68],"but":[69],"slow-search":[70],"algorithms":[71],"challenged":[73],"deliver":[75],"results":[76],"a":[78,93,106,150,155],"reasonable":[79],"time,":[80],"as":[81,113],"there":[82],"now":[84],"more":[85],"PDB":[89],"than":[90],"seconds":[91],"day.":[94],"brute-force":[96],"solution":[97],"would":[98],"be":[99,175],"distribute":[101],"individual":[103],"comparisons":[104],"on":[105,154],"massively":[107],"parallel":[108],"computer.":[109],"A":[110],"frugal":[111],"solution,":[112],"implemented":[114],"Dali":[117,159],"server,":[118],"is":[119,168],"reduce":[121],"total":[123],"computational":[124],"cost":[125],"pruning":[127],"search":[128],"space":[129],"prior":[131],"knowledge":[132,151],"about":[133],"distribution":[135],"fold":[139],"space.":[140],"This":[141],"note":[142],"reports":[143],"paradigm":[144],"revisions":[145],"enable":[147],"maintaining":[148],"such":[149],"base":[152],"up-to-date":[153],"PC.":[156],"AVAILABILITY:":[157],"server":[160],"for":[161,177],"structure":[163],"database":[164],"searching":[165],"at":[166],"http://ekhidna.biocenter.helsinki.fi/dali_server":[167],"DaliLite":[170],"v.3.":[171],"software":[173],"downloaded":[176],"academic":[178],"use":[179],"from":[180],"http://ekhidna.biocenter.helsinki.fi/dali_lite/downloads/v3.":[181]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":42},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":16},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":24},{"year":2019,"cited_by_count":28},{"year":2018,"cited_by_count":38},{"year":2017,"cited_by_count":25},{"year":2016,"cited_by_count":37},{"year":2015,"cited_by_count":46},{"year":2014,"cited_by_count":60},{"year":2013,"cited_by_count":72},{"year":2012,"cited_by_count":93}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
