{"id":"https://openalex.org/W2761824204","doi":"https://doi.org/10.1109/cibcb.2017.8058535","title":"Improving de novo protein structure prediction using contact maps information","display_name":"Improving de novo protein structure prediction using contact maps information","publication_year":2017,"publication_date":"2017-08-01","ids":{"openalex":"https://openalex.org/W2761824204","doi":"https://doi.org/10.1109/cibcb.2017.8058535","mag":"2761824204"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2017.8058535","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2017.8058535","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5013063323","display_name":"Karina B. Santos","orcid":"https://orcid.org/0000-0001-9202-4584"},"institutions":[{"id":"https://openalex.org/I4210142352","display_name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica","ror":"https://ror.org/0498ekt05","country_code":"BR","type":"government","lineage":["https://openalex.org/I4210142352"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Karina B. Santos","raw_affiliation_strings":["The National Laboratory for Scientific Computing (LNCC), Petr\u00f3polis, RJ, Brazil"],"affiliations":[{"raw_affiliation_string":"The National Laboratory for Scientific Computing (LNCC), Petr\u00f3polis, RJ, Brazil","institution_ids":["https://openalex.org/I4210142352"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033682893","display_name":"Gregorio Rocha","orcid":"https://orcid.org/0000-0003-1149-175X"},"institutions":[{"id":"https://openalex.org/I4210142352","display_name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica","ror":"https://ror.org/0498ekt05","country_code":"BR","type":"government","lineage":["https://openalex.org/I4210142352"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Gregorio K. Rocha","raw_affiliation_strings":["The National Laboratory for Scientific Computing (LNCC), Petr\u00f3polis, RJ, Brazil"],"affiliations":[{"raw_affiliation_string":"The National Laboratory for Scientific Computing (LNCC), Petr\u00f3polis, RJ, Brazil","institution_ids":["https://openalex.org/I4210142352"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020129323","display_name":"F\u00e1bio Lima Cust\u00f3dio","orcid":"https://orcid.org/0000-0001-5134-2340"},"institutions":[{"id":"https://openalex.org/I4210142352","display_name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica","ror":"https://ror.org/0498ekt05","country_code":"BR","type":"government","lineage":["https://openalex.org/I4210142352"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Fabio L. Custodio","raw_affiliation_strings":["The National Laboratory for Scientific Computing (LNCC), Petr\u00f3polis, RJ, Brazil"],"affiliations":[{"raw_affiliation_string":"The National Laboratory for Scientific Computing (LNCC), Petr\u00f3polis, RJ, Brazil","institution_ids":["https://openalex.org/I4210142352"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052002490","display_name":"H\u00e9lio J. C. Barbosa","orcid":"https://orcid.org/0000-0001-5810-7554"},"institutions":[{"id":"https://openalex.org/I4210142352","display_name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica","ror":"https://ror.org/0498ekt05","country_code":"BR","type":"government","lineage":["https://openalex.org/I4210142352"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Helio J. C. Barbosa","raw_affiliation_strings":["The National Laboratory for Scientific Computing (LNCC), Petr\u00f3polis, RJ, Brazil"],"affiliations":[{"raw_affiliation_string":"The National Laboratory for Scientific Computing (LNCC), Petr\u00f3polis, RJ, Brazil","institution_ids":["https://openalex.org/I4210142352"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084969079","display_name":"Laurent E. Dardenne","orcid":"https://orcid.org/0000-0001-8518-8062"},"institutions":[{"id":"https://openalex.org/I4210142352","display_name":"Laborat\u00f3rio Nacional de Computa\u00e7\u00e3o Cient\u00edfica","ror":"https://ror.org/0498ekt05","country_code":"BR","type":"government","lineage":["https://openalex.org/I4210142352"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Laurent E. Dardenne","raw_affiliation_strings":["The National Laboratory for Scientific Computing (LNCC), Petr\u00f3polis, RJ, Brazil"],"affiliations":[{"raw_affiliation_string":"The National Laboratory for Scientific Computing (LNCC), Petr\u00f3polis, RJ, Brazil","institution_ids":["https://openalex.org/I4210142352"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5013063323"],"corresponding_institution_ids":["https://openalex.org/I4210142352"],"apc_list":null,"apc_paid":null,"fwci":0.1063,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.49007054,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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":0.9995999932289124,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9815999865531921,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9815999865531921,"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/casp","display_name":"CASP","score":0.8842647075653076},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.6288869380950928},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.54671311378479},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3603529632091522},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12684577703475952}],"concepts":[{"id":"https://openalex.org/C66153294","wikidata":"https://www.wikidata.org/wiki/Q899291","display_name":"CASP","level":4,"score":0.8842647075653076},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.6288869380950928},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.54671311378479},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3603529632091522},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12684577703475952},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/cibcb.2017.8058535","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2017.8058535","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1493324970","https://openalex.org/W1540530720","https://openalex.org/W1901005744","https://openalex.org/W1910631782","https://openalex.org/W1946569870","https://openalex.org/W1988695007","https://openalex.org/W2006332277","https://openalex.org/W2007201984","https://openalex.org/W2013425283","https://openalex.org/W2014050554","https://openalex.org/W2107867854","https://openalex.org/W2110510374","https://openalex.org/W2114340287","https://openalex.org/W2136799255","https://openalex.org/W2139447922","https://openalex.org/W2145991251","https://openalex.org/W2152013549","https://openalex.org/W2153187042","https://openalex.org/W2154942971","https://openalex.org/W2208236301","https://openalex.org/W2275780625","https://openalex.org/W2280207768","https://openalex.org/W2345242111","https://openalex.org/W2395745621","https://openalex.org/W2524386004","https://openalex.org/W2574528486","https://openalex.org/W2949867299","https://openalex.org/W6639806595","https://openalex.org/W6676489643"],"related_works":["https://openalex.org/W2946599741","https://openalex.org/W1888349473","https://openalex.org/W2147472674","https://openalex.org/W2561391236","https://openalex.org/W2136856901","https://openalex.org/W3165545667","https://openalex.org/W4225106352","https://openalex.org/W47248631","https://openalex.org/W3171039768","https://openalex.org/W2058542300"],"abstract_inverted_index":{"The":[0,23,151],"use":[1,47,176],"of":[2,25,34,58,81,92,171,177,205],"residue-residue":[3,69],"contact":[4,39,49,74,112,125,137,157,178],"maps":[5,40,53,113,179],"in":[6,62,78,107,145,160,168],"protein":[7,98],"structure":[8,132],"prediction":[9],"(PSP)":[10],"has":[11],"proved":[12],"promising":[13],"during":[14],"the":[15,35,48,56,59,79,89,93,118,130,141,156,161,169,172,175,193,203],"last":[16],"CASP":[17],"editions":[18],"(CASP10,":[19],"11":[20],"and":[21,41,201],"12).":[22],"goals":[24],"this":[26],"work":[27],"are":[28],"to":[29,42,46,54,88,116,195,199],"carry":[30],"out":[31],"an":[32,165],"assessment":[33],"information":[36,72,204],"given":[37],"by":[38,149],"develop":[43,196],"a":[44,63,101,108,123,135,146,181],"strategy":[45,183],"constraints":[50],"from":[51,73,129],"these":[52],"improve":[55],"quality":[57],"predicted":[60,148,206],"models":[61],"de":[64,185],"novo":[65,186],"PSP":[66,187],"approach.":[67,110],"A":[68],"potential,":[70],"with":[71,104,139],"maps,":[75],"is":[76,86],"proposed":[77],"form":[80],"distance":[82],"constraints.":[83],"This":[84],"potential":[85,119,158],"added":[87],"fitness":[90],"function":[91],"GAPF":[94,162],"program,":[95],"which":[96],"predicts":[97],"structures":[99],"using":[100],"genetic":[102],"algorithm":[103],"phenotypic":[105],"crowding":[106],"free-modeling":[109],"Two":[111],"were":[114],"generated":[115],"evaluate":[117],"developed":[120],"here:":[121],"(i)":[122],"native":[124,142],"map":[126,138,147],"obtained":[127],"directly":[128],"experimental":[131],"and,":[133],"(ii)":[134],"filtered":[136],"only":[140],"contacts":[143],"present":[144],"MetaPSICOV.":[150],"experiments":[152],"performed":[153],"indicate":[154],"that":[155],"implemented":[159],"program":[163],"promoted":[164],"important":[166],"improvement":[167],"accuracy":[170],"predictions,":[173],"confirming":[174],"as":[180],"useful":[182],"for":[184],"methodologies.":[188],"Our":[189],"results":[190],"also":[191],"stress":[192],"need":[194],"better":[197],"strategies":[198],"filter":[200],"enhance":[202],"contacts.":[207]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}