{"id":"https://openalex.org/W2954851300","doi":"https://doi.org/10.1093/bioinformatics/btz536","title":"Benchmarking fold detection by DaliLite v.5","display_name":"Benchmarking fold detection by DaliLite v.5","publication_year":2019,"publication_date":"2019-06-28","ids":{"openalex":"https://openalex.org/W2954851300","doi":"https://doi.org/10.1093/bioinformatics/btz536","mag":"2954851300","pmid":"https://pubmed.ncbi.nlm.nih.gov/31263867"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz536","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz536","pdf_url":null,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"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"]},{"id":"https://openalex.org/I4210099114","display_name":"Czech Academy of Sciences, Institute of Biotechnology","ror":"https://ror.org/00wzqmx94","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210099114"]},{"id":"https://openalex.org/I4210118921","display_name":"Institute of Life Sciences","ror":"https://ror.org/02927dx12","country_code":"IN","type":"education","lineage":["https://openalex.org/I2799351866","https://openalex.org/I4210118921","https://openalex.org/I4210134808"]},{"id":"https://openalex.org/I4391768107","display_name":"HiLIFE \u2013 El\u00e4m\u00e4ntieteiden Instituutti","ror":"https://ror.org/018bh0m68","country_code":null,"type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I4391768107"]}],"countries":["CZ","FI","IN"],"is_corresponding":true,"raw_author_name":"Liisa Holm","raw_affiliation_strings":["Institute of Biotechnology, Helsinki Institute of Life Sciences","University of Helsinki Organismal and Evolutionary Biology Research Program, Faculty of Biosciences, , Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Helsinki Institute of Life Sciences","institution_ids":["https://openalex.org/I4210099114","https://openalex.org/I4210118921","https://openalex.org/I4391768107"]},{"raw_affiliation_string":"University of Helsinki Organismal and Evolutionary Biology Research Program, Faculty of Biosciences, , Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5064498279"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I4210099114","https://openalex.org/I4210118921","https://openalex.org/I4391768107"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":22.4616,"has_fulltext":false,"cited_by_count":342,"citation_normalized_percentile":{"value":0.99747184,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"35","issue":"24","first_page":"5326","last_page":"5327"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.501800000667572,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.501800000667572,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.19020000100135803,"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":0.08869999647140503,"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/benchmarking","display_name":"Benchmarking","score":0.8388993740081787},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7228949069976807},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6681674122810364},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.6462502479553223},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5278803110122681},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.4753398895263672},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.43067458271980286},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42721399664878845},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3739546537399292},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2915251851081848}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8388993740081787},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7228949069976807},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6681674122810364},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6462502479553223},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5278803110122681},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.4753398895263672},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.43067458271980286},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42721399664878845},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3739546537399292},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2915251851081848},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz536","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz536","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31263867","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31263867","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}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.5199999809265137}],"awards":[],"funders":[{"id":"https://openalex.org/F4320310086","display_name":"Helsingin Yliopisto","ror":"https://ror.org/040af2s02"},{"id":"https://openalex.org/F4320333873","display_name":"Helsinki Institute of Life Science, Helsingin Yliopisto","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W2022058405","https://openalex.org/W2090617952","https://openalex.org/W2102245393","https://openalex.org/W2110397834","https://openalex.org/W2137955461","https://openalex.org/W2142678478","https://openalex.org/W2161072217","https://openalex.org/W2796882337","https://openalex.org/W2804736431","https://openalex.org/W6751324841"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W4399363378"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein":[1],"structure":[2,33],"comparison":[3],"plays":[4],"a":[5,18,67,139],"fundamental":[6],"role":[7],"in":[8],"understanding":[9],"the":[10,22,32,94,110,125,133,136],"evolutionary":[11],"relationships":[12],"between":[13,141],"proteins.":[14],"Here,":[15],"we":[16],"release":[17],"new":[19],"version":[20],"of":[21,31,47,52,93,112,135],"DaliLite":[23,60,83,97],"standalone":[24],"software.":[25],"The":[26,50,116,128],"novelties":[27],"are":[28,153],"hierarchical":[29,126],"search":[30,74,118,130],"database":[34],"organized":[35],"into":[36],"sequence":[37],"based":[38,88],"clusters,":[39],"and":[40,55,61,84,96,104,143],"remote":[41],"access":[42],"to":[43,109],"our":[44],"knowledge":[45],"base":[46],"structural":[48,70],"neighbors.":[49],"detection":[51],"fold,":[53],"superfamily":[54],"family":[56],"level":[57],"similarities":[58],"by":[59],"state-of-the-art":[62],"competitors":[63],"was":[64,119],"benchmarked":[65],"against":[66],"manually":[68],"curated":[69],"classification.":[71],"RESULTS:":[72],"Database":[73],"strategies":[75],"were":[76],"evaluated":[77],"using":[78],"Fmax":[79],"with":[80],"query-specific":[81],"thresholds.":[82],"DeepAlign":[85,99],"outperformed":[86,98],"TM-score":[87],"methods":[89],"at":[90,100,155],"all":[91],"levels":[92],"benchmark,":[95],"fold":[101],"level.":[102],"Hierarchical":[103],"knowledge-based":[105,117,129],"searches":[106],"got":[107],"close":[108],"performance":[111],"systematic":[113],"pairwise":[114],"comparison.":[115],"four":[120],"times":[121],"as":[122,124],"efficient":[123],"search.":[127],"dynamically":[131],"adjusts":[132],"depth":[134],"search,":[137],"enabling":[138],"trade-off":[140],"speed":[142],"recall.":[144],"AVAILABILITY":[145],"AND":[146],"IMPLEMENTATION:":[147],"http://ekhidna2.biocenter.helsinki.fi/dali/README.v5.html.":[148],"SUPPLEMENTARY":[149],"INFORMATION:":[150],"Supplementary":[151],"data":[152],"available":[154],"Bioinformatics":[156],"online.":[157]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":22},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":22},{"year":2022,"cited_by_count":31},{"year":2021,"cited_by_count":74},{"year":2020,"cited_by_count":146},{"year":2019,"cited_by_count":21}],"updated_date":"2026-07-25T09:21:30.201066","created_date":"2025-10-10T00:00:00"}
