{"id":"https://openalex.org/W2978380288","doi":"https://doi.org/10.1093/bioinformatics/btz743","title":"Fast and flexible coarse-grained prediction of protein folding routes using ensemble modeling and evolutionary sequence variation","display_name":"Fast and flexible coarse-grained prediction of protein folding routes using ensemble modeling and evolutionary sequence variation","publication_year":2019,"publication_date":"2019-09-29","ids":{"openalex":"https://openalex.org/W2978380288","doi":"https://doi.org/10.1093/bioinformatics/btz743","mag":"2978380288","pmid":"https://pubmed.ncbi.nlm.nih.gov/31584628"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz743","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz743","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/5/1420/32794008/btz743.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":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/5/1420/32794008/btz743.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014250066","display_name":"David Becerra","orcid":"https://orcid.org/0000-0002-6944-916X"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"David Becerra","raw_affiliation_strings":["School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011936006","display_name":"Alexander Butyaev","orcid":"https://orcid.org/0009-0005-8028-0915"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Alexander Butyaev","raw_affiliation_strings":["School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada","institution_ids":["https://openalex.org/I5023651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000881484","display_name":"J\u00e9r\u00f4me Waldisp\u00fchl","orcid":"https://orcid.org/0000-0002-2561-7117"},"institutions":[{"id":"https://openalex.org/I5023651","display_name":"McGill University","ror":"https://ror.org/01pxwe438","country_code":"CA","type":"education","lineage":["https://openalex.org/I5023651"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"J\u00e9r\u00f4me Waldisp\u00fchl","raw_affiliation_strings":["School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, McGill University , Montr\u00e9al, QC H3A 0E9, Canada","institution_ids":["https://openalex.org/I5023651"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5000881484"],"corresponding_institution_ids":["https://openalex.org/I5023651"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0759,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.43257896,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"36","issue":"5","first_page":"1420","last_page":"1428"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.7666000127792358,"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":0.7666000127792358,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.06019999831914902,"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":0.039799999445676804,"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":0.7721778750419617},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.6359588503837585},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.5382815003395081},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.48931118845939636},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35831448435783386},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.22154536843299866},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.11226633191108704}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7721778750419617},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.6359588503837585},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5382815003395081},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.48931118845939636},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35831448435783386},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.22154536843299866},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11226633191108704},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","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/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":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":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz743","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz743","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/5/1420/32794008/btz743.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:31584628","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31584628","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":{"id":"doi:10.1093/bioinformatics/btz743","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz743","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/5/1420/32794008/btz743.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":[{"id":"https://metadata.un.org/sdg/15","score":0.6700000166893005,"display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W192510599","https://openalex.org/W837523969","https://openalex.org/W1505900198","https://openalex.org/W1570122994","https://openalex.org/W1970769480","https://openalex.org/W1973546204","https://openalex.org/W1975362548","https://openalex.org/W1975969507","https://openalex.org/W1982500800","https://openalex.org/W1982789149","https://openalex.org/W1994267130","https://openalex.org/W2011277157","https://openalex.org/W2014050554","https://openalex.org/W2030384127","https://openalex.org/W2037492941","https://openalex.org/W2046767590","https://openalex.org/W2048469982","https://openalex.org/W2067236515","https://openalex.org/W2075460992","https://openalex.org/W2082759836","https://openalex.org/W2085212975","https://openalex.org/W2088809689","https://openalex.org/W2093617347","https://openalex.org/W2096933265","https://openalex.org/W2101247857","https://openalex.org/W2102277886","https://openalex.org/W2104145621","https://openalex.org/W2108102848","https://openalex.org/W2131395827","https://openalex.org/W2137209317","https://openalex.org/W2137841361","https://openalex.org/W2139236870","https://openalex.org/W2153131823","https://openalex.org/W2153140501","https://openalex.org/W2161193937","https://openalex.org/W2163940928","https://openalex.org/W2165768701","https://openalex.org/W2343931134","https://openalex.org/W2475449190","https://openalex.org/W2771559100","https://openalex.org/W2901105999","https://openalex.org/W4233269677"],"related_works":["https://openalex.org/W2260493136","https://openalex.org/W2113188411","https://openalex.org/W4210423528","https://openalex.org/W2976965029","https://openalex.org/W2023600921","https://openalex.org/W2382178265","https://openalex.org/W2055827177","https://openalex.org/W2072666835","https://openalex.org/W4248706500","https://openalex.org/W2939859775"],"abstract_inverted_index":{"MOTIVATION:":[0],"Protein":[1],"folding":[2,58,75],"is":[3,22,144],"a":[4,42,78],"dynamic":[5],"process":[6],"through":[7],"which":[8],"polypeptide":[9],"chains":[10],"reach":[11],"their":[12],"native":[13],"3D":[14],"structures.":[15],"Although":[16],"the":[17,74,120,125],"importance":[18],"of":[19,77,130,142],"this":[20,38,89],"mechanism":[21],"widely":[23],"acknowledged,":[24],"very":[25],"few":[26],"high-throughput":[27],"computational":[28,43],"methods":[29],"have":[30],"been":[31],"developed":[32],"to":[33,68,88,104,112],"study":[34],"it.":[35],"RESULTS:":[36],"In":[37],"paper,":[39],"we":[40,91,109],"report":[41],"platform":[44],"named":[45],"P3Fold":[46,60,106,111,143],"that":[47,101,123],"combines":[48],"statistical":[49],"and":[50,55,64,72,95,115,128],"evolutionary":[51],"information":[52],"for":[53],"predicting":[54],"analyzing":[56],"protein":[57,79,134],"routes.":[59],"uses":[61],"coarse-grained":[62],"modeling":[63],"efficient":[65],"combinatorial":[66],"schemes":[67],"predict":[69],"residue":[70],"contacts":[71],"evaluate":[73],"routes":[76],"sequence":[80],"within":[81,133],"minutes":[82],"or":[83],"hours.":[84],"To":[85],"facilitate":[86],"access":[87],"technology,":[90],"devise":[92],"graphical":[93],"representations":[94],"implement":[96],"an":[97],"interactive":[98],"web":[99],"interface":[100],"allows":[102],"end-users":[103],"leverage":[105],"predictions.":[107],"Finally,":[108],"use":[110],"conduct":[113],"large":[114],"short":[116],"scale":[117],"experiments":[118],"on":[119],"human":[121],"proteome":[122],"reveal":[124],"broad":[126],"conservation":[127],"variations":[129],"structural":[131],"intermediates":[132],"families.":[135],"AVAILABILITY":[136],"AND":[137],"IMPLEMENTATION:":[138],"A":[139],"Web":[140],"server":[141],"freely":[145],"available":[146,154],"at":[147,155],"http://csb.cs.mcgill.ca/P3Fold.":[148],"SUPPLEMENTARY":[149],"INFORMATION:":[150],"Supplementary":[151],"data":[152],"are":[153],"Bioinformatics":[156],"online.":[157]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2021,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}