{"id":"https://openalex.org/W2139310526","doi":"https://doi.org/10.1093/bioinformatics/btt530","title":"Protein evolution along phylogenetic histories under structurally constrained substitution models","display_name":"Protein evolution along phylogenetic histories under structurally constrained substitution models","publication_year":2013,"publication_date":"2013-09-12","ids":{"openalex":"https://openalex.org/W2139310526","doi":"https://doi.org/10.1093/bioinformatics/btt530","mag":"2139310526","pmid":"https://pubmed.ncbi.nlm.nih.gov/24037213"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt530","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt530","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":true,"oa_status":"green","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/23/3020/48898788/bioinformatics_29_23_3020.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037761662","display_name":"Miguel Arenas","orcid":"https://orcid.org/0000-0002-0516-2717"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"funder","lineage":["https://openalex.org/I134820265"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Miguel Arenas","raw_affiliation_strings":["1 Centre for Molecular Biology \u2018Severo Ochoa\u2019, Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Madrid, Spain and 2Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain"],"affiliations":[{"raw_affiliation_string":"1 Centre for Molecular Biology \u2018Severo Ochoa\u2019, Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Madrid, Spain and 2Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain","institution_ids":["https://openalex.org/I6289922","https://openalex.org/I134820265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000462747","display_name":"Helena G. Dos Santos","orcid":"https://orcid.org/0000-0002-9671-4272"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"funder","lineage":["https://openalex.org/I134820265"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Helena G. Dos Santos","raw_affiliation_strings":["1 Centre for Molecular Biology \u2018Severo Ochoa\u2019, Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Madrid, Spain and 2Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain"],"affiliations":[{"raw_affiliation_string":"1 Centre for Molecular Biology \u2018Severo Ochoa\u2019, Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Madrid, Spain and 2Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain","institution_ids":["https://openalex.org/I6289922","https://openalex.org/I134820265"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042649313","display_name":"David Posada","orcid":"https://orcid.org/0000-0003-1407-3406"},"institutions":[{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"funder","lineage":["https://openalex.org/I134820265"]},{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"David Posada","raw_affiliation_strings":["1 Centre for Molecular Biology \u2018Severo Ochoa\u2019, Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Madrid, Spain and 2Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain"],"affiliations":[{"raw_affiliation_string":"1 Centre for Molecular Biology \u2018Severo Ochoa\u2019, Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Madrid, Spain and 2Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain","institution_ids":["https://openalex.org/I6289922","https://openalex.org/I134820265"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013334733","display_name":"Ugo Bastolla","orcid":"https://orcid.org/0000-0001-9342-4678"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"id":"https://openalex.org/I134820265","display_name":"Consejo Superior de Investigaciones Cient\u00edficas","ror":"https://ror.org/02gfc7t72","country_code":"ES","type":"funder","lineage":["https://openalex.org/I134820265"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Ugo Bastolla","raw_affiliation_strings":["1 Centre for Molecular Biology \u2018Severo Ochoa\u2019, Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Madrid, Spain and 2Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain"],"affiliations":[{"raw_affiliation_string":"1 Centre for Molecular Biology \u2018Severo Ochoa\u2019, Consejo Superior de Investigaciones Cient\u00edficas (CSIC), Madrid, Spain and 2Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain","institution_ids":["https://openalex.org/I6289922","https://openalex.org/I134820265"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5037761662"],"corresponding_institution_ids":["https://openalex.org/I134820265","https://openalex.org/I6289922"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.3918,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.89082391,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"29","issue":"23","first_page":"3020","last_page":"3028"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983000159263611,"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":0.9983000159263611,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973999857902527,"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":0.9932000041007996,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6978359818458557},{"id":"https://openalex.org/keywords/protein-evolution","display_name":"Protein evolution","score":0.5938376784324646},{"id":"https://openalex.org/keywords/coalescent-theory","display_name":"Coalescent theory","score":0.5855205655097961},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5658812522888184},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.5578615069389343},{"id":"https://openalex.org/keywords/evolutionary-algorithm","display_name":"Evolutionary algorithm","score":0.5347952246665955},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.5208090543746948},{"id":"https://openalex.org/keywords/substitution","display_name":"Substitution (logic)","score":0.4844546318054199},{"id":"https://openalex.org/keywords/molecular-evolution","display_name":"Molecular evolution","score":0.4737342596054077},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.46756988763809204},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.4646551012992859},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.33017459511756897},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3023582994937897},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25431668758392334},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2296629250049591},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15896058082580566}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6978359818458557},{"id":"https://openalex.org/C2992240565","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Protein evolution","level":3,"score":0.5938376784324646},{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.5855205655097961},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5658812522888184},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.5578615069389343},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.5347952246665955},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5208090543746948},{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.4844546318054199},{"id":"https://openalex.org/C166393388","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Molecular evolution","level":4,"score":0.4737342596054077},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.46756988763809204},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4646551012992859},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.33017459511756897},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3023582994937897},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25431668758392334},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2296629250049591},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15896058082580566},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","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":"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btt530","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt530","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:24037213","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24037213","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:www.investigo.biblioteca.uvigo.es:11093/5619","is_oa":true,"landing_page_url":"http://hdl.handle.net/11093/5619","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/23/3020/48898788/bioinformatics_29_23_3020.pdf","source":{"id":"https://openalex.org/S4377196408","display_name":"Investigo Institutional repository of UVigo (Universidade de Vigo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I6289922","host_organization_name":"Universidade de Vigo","host_organization_lineage":["https://openalex.org/I6289922"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},{"id":"pmh:oai:digital.csic.es:10261/98395","is_oa":false,"landing_page_url":"http://hdl.handle.net/10261/98395","pdf_url":null,"source":{"id":"https://openalex.org/S4306400616","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"art\u00edculo"},{"id":"pmh:oai:pubmedcentral.nih.gov:5221705","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5221705","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:www.investigo.biblioteca.uvigo.es:11093/5619","is_oa":true,"landing_page_url":"http://hdl.handle.net/11093/5619","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/23/3020/48898788/bioinformatics_29_23_3020.pdf","source":{"id":"https://openalex.org/S4377196408","display_name":"Investigo Institutional repository of UVigo (Universidade de Vigo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I6289922","host_organization_name":"Universidade de Vigo","host_organization_lineage":["https://openalex.org/I6289922"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2139310526.pdf"},"referenced_works_count":76,"referenced_works":["https://openalex.org/W114397555","https://openalex.org/W161323843","https://openalex.org/W420957490","https://openalex.org/W590116524","https://openalex.org/W1492846538","https://openalex.org/W1525240758","https://openalex.org/W1585006589","https://openalex.org/W1607931568","https://openalex.org/W1886080132","https://openalex.org/W1973595229","https://openalex.org/W1980458832","https://openalex.org/W1988644414","https://openalex.org/W1989893963","https://openalex.org/W1990823383","https://openalex.org/W1992579032","https://openalex.org/W1993900316","https://openalex.org/W1999613945","https://openalex.org/W2003644562","https://openalex.org/W2011754703","https://openalex.org/W2013437827","https://openalex.org/W2014690416","https://openalex.org/W2015470526","https://openalex.org/W2018948884","https://openalex.org/W2019000267","https://openalex.org/W2019956985","https://openalex.org/W2024997496","https://openalex.org/W2032096575","https://openalex.org/W2041938888","https://openalex.org/W2046956642","https://openalex.org/W2055898129","https://openalex.org/W2065283382","https://openalex.org/W2071700760","https://openalex.org/W2075110982","https://openalex.org/W2080473579","https://openalex.org/W2083715726","https://openalex.org/W2088349342","https://openalex.org/W2092387745","https://openalex.org/W2092727091","https://openalex.org/W2093731904","https://openalex.org/W2096619551","https://openalex.org/W2096993581","https://openalex.org/W2097136496","https://openalex.org/W2106549255","https://openalex.org/W2108675597","https://openalex.org/W2112607023","https://openalex.org/W2113551702","https://openalex.org/W2114520383","https://openalex.org/W2116209557","https://openalex.org/W2116416291","https://openalex.org/W2119592647","https://openalex.org/W2130007916","https://openalex.org/W2130824586","https://openalex.org/W2133549457","https://openalex.org/W2135825004","https://openalex.org/W2136655076","https://openalex.org/W2137480875","https://openalex.org/W2141470483","https://openalex.org/W2144654387","https://openalex.org/W2144901174","https://openalex.org/W2150842476","https://openalex.org/W2155836971","https://openalex.org/W2157362913","https://openalex.org/W2162025818","https://openalex.org/W2165892911","https://openalex.org/W2169882791","https://openalex.org/W2208088588","https://openalex.org/W2315686940","https://openalex.org/W2591756625","https://openalex.org/W2883755802","https://openalex.org/W3023590112","https://openalex.org/W3140456911","https://openalex.org/W4210633230","https://openalex.org/W4230357098","https://openalex.org/W4243131309","https://openalex.org/W4245153032","https://openalex.org/W6645331517"],"related_works":["https://openalex.org/W2011606533","https://openalex.org/W2119438568","https://openalex.org/W2417800113","https://openalex.org/W1967807546","https://openalex.org/W2000440788","https://openalex.org/W3150126673","https://openalex.org/W2904459719","https://openalex.org/W4281698698","https://openalex.org/W2075292448","https://openalex.org/W2978410946"],"abstract_inverted_index":{"We":[0,59],"developed":[1],"a":[2,65,121],"method":[3],"to":[4,30,90,102],"simulate":[5],"protein":[6,12,95,114],"evolution":[7],"that":[8,16,37,82,99,109,112],"combines":[9],"models":[10,73,111],"of":[11,23,124],"folding":[13],"stability,":[14],"such":[15],"the":[17,21,24,43,48,83,125],"fitness":[18],"depends":[19],"on":[20],"stability":[22,115],"native":[25],"state":[26],"both":[27],"with":[28,34,47,74],"respect":[29],"unfolding":[31],"and":[32,57,97,116],"misfolding,":[33],"phylogenetic":[35],"histories":[36,119],"can":[38],"be":[39,103],"either":[40],"specified":[41],"by":[42],"user":[44],"or":[45],"simulated":[46],"coalescent":[49],"under":[50],"complex":[51],"evolutionary":[52,110,118,127],"scenarios,":[53],"including":[54],"recombination,":[55],"demographics":[56],"migration.":[58],"have":[60],"implemented":[61],"this":[62],"framework":[63],"in":[64,93],"computer":[66],"program":[67],"called":[68],"ProteinEvolver.":[69],"Remarkably,":[70],"comparing":[71],"these":[72],"empirical":[75],"amino":[76,86],"acid":[77,87],"replacement":[78],"models,":[79],"we":[80,107],"found":[81],"former":[84],"produce":[85],"distributions":[88,91],"closer":[89],"observed":[92],"real":[94,126],"families,":[96],"proteins":[98],"are":[100],"predicted":[101],"more":[104],"stable.":[105],"Therefore,":[106],"conclude":[108],"consider":[113],"realistic":[117],"constitute":[120],"better":[122],"approximation":[123],"process.":[128]},"counts_by_year":[{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
