{"id":"https://openalex.org/W2526778105","doi":"https://doi.org/10.1093/bioinformatics/btw628","title":"Granular clustering of <i>de novo</i> protein models","display_name":"Granular clustering of <i>de novo</i> protein models","publication_year":2016,"publication_date":"2016-09-29","ids":{"openalex":"https://openalex.org/W2526778105","doi":"https://doi.org/10.1093/bioinformatics/btw628","mag":"2526778105","pmid":"https://pubmed.ncbi.nlm.nih.gov/28171609"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw628","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw628","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/3/390/25146012/btw628.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/3/390/25146012/btw628.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013018624","display_name":"Dmytro Guzenko","orcid":"https://orcid.org/0000-0002-8688-7460"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Dmytro Guzenko","raw_affiliation_strings":["Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007438759","display_name":"Sergei V. Strelkov","orcid":"https://orcid.org/0000-0001-7189-4652"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Sergei V Strelkov","raw_affiliation_strings":["Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5007438759"],"corresponding_institution_ids":["https://openalex.org/I99464096"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3417,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.68773061,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"33","issue":"3","first_page":"390","last_page":"396"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.4950999915599823,"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":0.4950999915599823,"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":0.19339999556541443,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.05249999836087227,"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/cluster-analysis","display_name":"Cluster analysis","score":0.7903982400894165},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7273020148277283},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6703339219093323},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5228312611579895},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4773564338684082},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4735540449619293},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.47198039293289185},{"id":"https://openalex.org/keywords/phaser","display_name":"Phaser","score":0.4684567451477051},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.44624632596969604},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32188183069229126},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.31815218925476074},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3112354874610901},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1122010350227356},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08671256899833679},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.08620798587799072}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7903982400894165},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7273020148277283},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6703339219093323},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5228312611579895},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4773564338684082},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4735540449619293},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.47198039293289185},{"id":"https://openalex.org/C135393689","wikidata":"https://www.wikidata.org/wiki/Q1551588","display_name":"Phaser","level":2,"score":0.4684567451477051},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.44624632596969604},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32188183069229126},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.31815218925476074},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3112354874610901},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1122010350227356},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08671256899833679},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08620798587799072},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","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":"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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw628","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw628","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/3/390/25146012/btw628.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28171609","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28171609","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:lirias2repo.kuleuven.be:123456789/551808","is_oa":true,"landing_page_url":"https://lirias.kuleuven.be/handle/123456789/551808","pdf_url":null,"source":{"id":"https://openalex.org/S7407055369","display_name":"Lirias","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Bioinformatics, vol. 33 (3), (390-396)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:arXiv.org:1711.09242","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1711.09242","pdf_url":"https://arxiv.org/pdf/1711.09242","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw628","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw628","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/3/390/25146012/btw628.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1548178570","https://openalex.org/W2013792107","https://openalex.org/W2052963427","https://openalex.org/W2059429344","https://openalex.org/W2067191022","https://openalex.org/W2084327812","https://openalex.org/W2101234009","https://openalex.org/W2108921801","https://openalex.org/W2110483430","https://openalex.org/W2114383673","https://openalex.org/W2114850508","https://openalex.org/W2120132320","https://openalex.org/W2135066023","https://openalex.org/W2136567909","https://openalex.org/W2140564438","https://openalex.org/W2140673705","https://openalex.org/W2144213670","https://openalex.org/W2146134187","https://openalex.org/W2146886262","https://openalex.org/W2158698691","https://openalex.org/W2163341755","https://openalex.org/W2170203299","https://openalex.org/W2201713963","https://openalex.org/W4210309881","https://openalex.org/W4210586598","https://openalex.org/W4300802462","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W2003248827","https://openalex.org/W2946599741","https://openalex.org/W3199982763","https://openalex.org/W2593264178","https://openalex.org/W3171039768","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2058542300","https://openalex.org/W2043066834","https://openalex.org/W1564749278"],"abstract_inverted_index":{"Motivation:":[0],"Modern":[1],"algorithms":[2],"for":[3,53],"de":[4],"novo":[5],"prediction":[6],"of":[7,23,33,73,94,117,126,147],"protein":[8,49,139],"structures":[9],"typically":[10],"output":[11,155],"multiple":[12],"full-length":[13],"models":[14,50,68,96,128,154,172],"(decoys)":[15],"rather":[16],"than":[17,140],"a":[18,70,84,115,130,144],"single":[19],"solution.":[20],"Subsequent":[21],"clustering":[22,86,103],"such":[24,56],"decoys":[25],"is":[26,107,183],"used":[27],"both":[28],"to":[29,37,170],"gauge":[30],"the":[31,34,40,45,74,92,123,137,150,152,166,171],"success":[32],"modelling":[35],"and":[36,178],"decide":[38],"on":[39,109,136],"most":[41],"native-like":[42],"conformation.":[43],"At":[44],"same":[46],"time,":[47],"partial":[48,95,127,153],"are":[51,160,194],"sufficient":[52],"some":[54],"applications":[55],"as":[57,101],"crystallographic":[58],"phasing":[59],"by":[60,156,174],"molecular":[61],"replacement":[62],"(MR)":[63],"in":[64,91,114],"particular,":[65],"provided":[66],"these":[67],"represent":[69],"certain":[71],"part":[72],"target":[75,138],"structure":[76],"with":[77],"reasonable":[78],"accuracy.":[79],"Results:":[80],"Here":[81],"we":[82],"propose":[83],"novel":[85],"algorithm":[87,106,159],"that":[88,122],"natively":[89],"operates":[90],"space":[93],"through":[97],"an":[98],"approach":[99],"known":[100],"granular":[102],"(GC).":[104],"The":[105,180],"based":[108],"growing":[110],"local":[111],"similarities":[112],"found":[113],"pool":[116],"initial":[118],"decoys.":[119,148],"We":[120],"demonstrate":[121],"resulting":[124],"clusters":[125],"provide":[129],"substantially":[131],"more":[132,163],"accurate":[133],"structural":[134],"detail":[135],"those":[141],"obtained":[142],"upon":[143],"global":[145],"alignment":[146],"As":[149],"result,":[151],"our":[157],"GC":[158],"also":[161],"much":[162],"effective":[164],"towards":[165],"MR":[167],"procedure,":[168],"compared":[169],"produced":[173],"existing":[175],"software.":[176],"Availability":[177],"Implementation:":[179],"source":[181],"code":[182],"freely":[184],"available":[185,195],"at":[186,196],"https://github.com/biocryst/gc":[187],"Contact:":[188],"sergei.strelkov@kuleuven.be":[189],"Suplementary":[190],"Information:":[191],"Supplementary":[192],"data":[193],"Bioinformatics":[197],"online.":[198]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":2}],"updated_date":"2026-07-03T08:13:44.112507","created_date":"2016-10-07T00:00:00"}
