{"id":"https://openalex.org/W2937569020","doi":"https://doi.org/10.1093/nar/gkz288","title":"GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure","display_name":"GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure","publication_year":2019,"publication_date":"2019-04-11","ids":{"openalex":"https://openalex.org/W2937569020","doi":"https://doi.org/10.1093/nar/gkz288","mag":"2937569020","pmid":"https://pubmed.ncbi.nlm.nih.gov/31001635"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkz288","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz288","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W451/28880091/gkz288.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/47/W1/W451/28880091/gkz288.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081678768","display_name":"Gyu Rie Lee","orcid":"https://orcid.org/0000-0002-9119-5303"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Gyu Rie Lee","raw_affiliation_strings":["Department of Chemistry, Seoul National University, Seoul 08826, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Seoul National University, Seoul 08826, Korea","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044437309","display_name":"Jonghun Won","orcid":"https://orcid.org/0000-0002-4788-3686"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jonghun Won","raw_affiliation_strings":["Department of Chemistry, Seoul National University, Seoul 08826, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Seoul National University, Seoul 08826, Korea","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087087224","display_name":"Lim Heo","orcid":"https://orcid.org/0000-0002-3153-2363"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Lim Heo","raw_affiliation_strings":["Department of Chemistry, Seoul National University, Seoul 08826, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Seoul National University, Seoul 08826, Korea","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003116915","display_name":"Chaok Seok","orcid":null},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Chaok Seok","raw_affiliation_strings":["Department of Chemistry, Seoul National University, Seoul 08826, Korea"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Seoul National University, Seoul 08826, Korea","institution_ids":["https://openalex.org/I139264467"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5003116915"],"corresponding_institution_ids":["https://openalex.org/I139264467"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.4542,"has_fulltext":true,"cited_by_count":137,"citation_normalized_percentile":{"value":0.95564491,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"47","issue":"W1","first_page":"W451","last_page":"W455"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.996999979019165,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.996999979019165,"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":0.9969000220298767,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9959999918937683,"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":0.6879817843437195},{"id":"https://openalex.org/keywords/casp","display_name":"CASP","score":0.6515103578567505},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.5701317191123962},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5629079937934875},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.5146487951278687},{"id":"https://openalex.org/keywords/coevolution","display_name":"Coevolution","score":0.5131171345710754},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.47952961921691895},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.47610270977020264},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.473032683134079},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.42960089445114136},{"id":"https://openalex.org/keywords/local-structure","display_name":"Local structure","score":0.4279901087284088},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.41803622245788574},{"id":"https://openalex.org/keywords/protein-secondary-structure","display_name":"Protein secondary structure","score":0.41312867403030396},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4069482982158661},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.28371044993400574},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20574453473091125},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1390383243560791},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.10678154230117798},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.1012536883354187},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.0993373692035675}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6879817843437195},{"id":"https://openalex.org/C66153294","wikidata":"https://www.wikidata.org/wiki/Q899291","display_name":"CASP","level":4,"score":0.6515103578567505},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.5701317191123962},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5629079937934875},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.5146487951278687},{"id":"https://openalex.org/C33009525","wikidata":"https://www.wikidata.org/wiki/Q208841","display_name":"Coevolution","level":2,"score":0.5131171345710754},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.47952961921691895},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.47610270977020264},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.473032683134079},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.42960089445114136},{"id":"https://openalex.org/C2986090443","wikidata":"https://www.wikidata.org/wiki/Q77870413","display_name":"Local structure","level":2,"score":0.4279901087284088},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.41803622245788574},{"id":"https://openalex.org/C62614982","wikidata":"https://www.wikidata.org/wiki/Q904984","display_name":"Protein secondary structure","level":2,"score":0.41312867403030396},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4069482982158661},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.28371044993400574},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20574453473091125},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1390383243560791},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.10678154230117798},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.1012536883354187},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.0993373692035675},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.0}],"mesh":[{"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":"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":"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":3,"locations":[{"id":"doi:10.1093/nar/gkz288","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz288","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W451/28880091/gkz288.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:31001635","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31001635","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:5577246","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6602442","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"}],"best_oa_location":{"id":"doi:10.1093/nar/gkz288","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkz288","pdf_url":"https://academic.oup.com/nar/article-pdf/47/W1/W451/28880091/gkz288.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/G1188491866","display_name":null,"funder_award_id":"2016M3C4A7952630","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G5145546482","display_name":null,"funder_award_id":"2016R1A2A1A05005485","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320321292","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2937569020.pdf","grobid_xml":"https://content.openalex.org/works/W2937569020.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1989777815","https://openalex.org/W1998917415","https://openalex.org/W2013425283","https://openalex.org/W2055043387","https://openalex.org/W2080876451","https://openalex.org/W2114520383","https://openalex.org/W2130060890","https://openalex.org/W2137604324","https://openalex.org/W2138894883","https://openalex.org/W2140673705","https://openalex.org/W2142319132","https://openalex.org/W2145268834","https://openalex.org/W2159155807","https://openalex.org/W2161151688","https://openalex.org/W2187538409","https://openalex.org/W2277366394","https://openalex.org/W2514674691","https://openalex.org/W2562930371","https://openalex.org/W2574496196","https://openalex.org/W2605158478","https://openalex.org/W2748834817","https://openalex.org/W2765362440","https://openalex.org/W2766793957","https://openalex.org/W2769882797","https://openalex.org/W2801109052","https://openalex.org/W2810170781","https://openalex.org/W2912932504","https://openalex.org/W2949867299","https://openalex.org/W3151623406","https://openalex.org/W4241935390","https://openalex.org/W6793593631"],"related_works":["https://openalex.org/W3171039768","https://openalex.org/W2153191110","https://openalex.org/W2136856901","https://openalex.org/W4206949911","https://openalex.org/W4205299763","https://openalex.org/W2557267299","https://openalex.org/W2913820882","https://openalex.org/W1564749278","https://openalex.org/W2032630890","https://openalex.org/W3004912075"],"abstract_inverted_index":{"The":[0,121,170],"3D":[1],"structure":[2,69,96,137,160],"of":[3,21,24,27,30,36,67,133,172,177],"a":[4,18,93],"protein":[5,51,95,136],"can":[6],"be":[7,109],"predicted":[8,73,94],"from":[9],"its":[10],"amino":[11],"acid":[12],"sequence":[13],"with":[14,97],"high":[15],"accuracy":[16],"for":[17,87,184],"large":[19,28],"fraction":[20],"cases":[22],"because":[23,105],"the":[25,34,44,65,134],"availability":[26],"quantities":[29],"experimental":[31],"data":[32],"and":[33,140,167,175],"advance":[35],"computational":[37],"algorithms.":[38],"Recently,":[39],"deep":[40],"learning":[41],"methods":[42],"exploiting":[43],"coevolution":[45],"information":[46,89,99],"obtained":[47],"by":[48],"comparing":[49],"related":[50,80,119],"sequences":[52,81],"have":[53],"been":[54],"successfully":[55,144],"used":[56],"to":[57,111,163],"generate":[58],"highly":[59],"accurate":[60],"model":[61],"structures":[62,72,78,180],"even":[63],"in":[64,85],"absence":[66],"template":[68,77],"information.":[70],"However,":[71],"based":[74],"on":[75,100],"either":[76],"or":[79],"require":[82],"further":[83],"improvement":[84],"regions":[86,102,107],"which":[88],"is":[90,103,115,129],"missing.":[91],"Refining":[92],"insufficient":[98],"certain":[101],"critical":[104],"these":[106],"may":[108],"connected":[110],"functional":[112],"specificity":[113],"that":[114],"not":[116],"conserved":[117],"among":[118],"proteins.":[120],"GalaxyRefine2":[122],"web":[123],"server,":[124],"freely":[125],"available":[126,178],"via":[127],"http://galaxy.seoklab.org/refine2,":[128],"an":[130,154],"upgraded":[131],"version":[132],"GalaxyRefine":[135],"refinement":[138],"server":[139],"reflects":[141],"recent":[142],"developments":[143],"tested":[145],"through":[146],"CASP":[147],"blind":[148],"prediction":[149],"experiments.":[150],"This":[151],"method":[152],"adopts":[153],"iterative":[155],"optimization":[156],"approach":[157],"involving":[158],"various":[159],"move":[161],"sets":[162],"refine":[164],"both":[165],"local":[166,173],"global":[168],"structures.":[169],"estimation":[171],"error":[174],"hybridization":[176],"homolog":[179],"are":[181],"also":[182],"employed":[183],"effective":[185],"conformation":[186],"search.":[187]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":38},{"year":2024,"cited_by_count":23},{"year":2023,"cited_by_count":18},{"year":2022,"cited_by_count":26},{"year":2021,"cited_by_count":16},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-28T08:17:26.163206","created_date":"2025-10-10T00:00:00"}
