{"id":"https://openalex.org/W4414493548","doi":"https://doi.org/10.1093/database/baaf052","title":"Empirical substitution models of protein evolution: database, relationships, and modeling considerations","display_name":"Empirical substitution models of protein evolution: database, relationships, and modeling considerations","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4414493548","doi":"https://doi.org/10.1093/database/baaf052","pmid":"https://pubmed.ncbi.nlm.nih.gov/40996708"},"language":"en","primary_location":{"id":"doi:10.1093/database/baaf052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaf052","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaf052/64394797/baaf052.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","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/database/article-pdf/doi/10.1093/database/baaf052/64394797/baaf052.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5119095486","display_name":"Paula Iglesias-Rivas","orcid":null},"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"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Paula Iglesias-Rivas","raw_affiliation_strings":["CINBIO, Universidade de Vigo , 36310 Vigo ,","Universidade de Vigo Department of Biochemistry, Genetics and Immunology, , 36310 Vigo ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CINBIO, Universidade de Vigo , 36310 Vigo ,","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"Universidade de Vigo Department of Biochemistry, Genetics and Immunology, , 36310 Vigo ,","institution_ids":["https://openalex.org/I6289922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080222368","display_name":"Roberto Del Amparo","orcid":"https://orcid.org/0000-0003-2189-1263"},"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"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Roberto Del\u00a0Amparo","raw_affiliation_strings":["CINBIO, Universidade de Vigo , 36310 Vigo ,","Universidade de Vigo Department of Biochemistry, Genetics and Immunology, , 36310 Vigo ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CINBIO, Universidade de Vigo , 36310 Vigo ,","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"Universidade de Vigo Department of Biochemistry, Genetics and Immunology, , 36310 Vigo ,","institution_ids":["https://openalex.org/I6289922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113681022","display_name":"J. Cabaleiro","orcid":null},"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"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Javier A Cabaleiro","raw_affiliation_strings":["CINBIO, Universidade de Vigo , 36310 Vigo ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CINBIO, Universidade de Vigo , 36310 Vigo ,","institution_ids":["https://openalex.org/I6289922"]}]},{"author_position":"last","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"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Miguel Arenas","raw_affiliation_strings":["CINBIO, Universidade de Vigo , 36310 Vigo ,","Universidade de Vigo Department of Biochemistry, Genetics and Immunology, , 36310 Vigo ,"],"raw_orcid":"https://orcid.org/0000-0002-0516-2717","affiliations":[{"raw_affiliation_string":"CINBIO, Universidade de Vigo , 36310 Vigo ,","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"Universidade de Vigo Department of Biochemistry, Genetics and Immunology, , 36310 Vigo ,","institution_ids":["https://openalex.org/I6289922"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5037761662"],"corresponding_institution_ids":["https://openalex.org/I6289922"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.818,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.72915326,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"2025","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9733999967575073,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9587000012397766,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/substitution","display_name":"Substitution (logic)","score":0.8758999705314636},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5349000096321106},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.5235999822616577},{"id":"https://openalex.org/keywords/amino-acid-substitution","display_name":"Amino acid substitution","score":0.482699990272522},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.47360000014305115},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4490000009536743},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.4230000078678131},{"id":"https://openalex.org/keywords/empirical-modelling","display_name":"Empirical modelling","score":0.40130001306533813},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.38830000162124634}],"concepts":[{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.8758999705314636},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5349000096321106},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5235999822616577},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4893999993801117},{"id":"https://openalex.org/C2993683473","wikidata":"https://www.wikidata.org/wiki/Q30693176","display_name":"Amino acid substitution","level":4,"score":0.482699990272522},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.47360000014305115},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4490000009536743},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.4230000078678131},{"id":"https://openalex.org/C133199616","wikidata":"https://www.wikidata.org/wiki/Q25386885","display_name":"Empirical modelling","level":2,"score":0.40130001306533813},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38989999890327454},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.38830000162124634},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.35899999737739563},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.35740000009536743},{"id":"https://openalex.org/C166393388","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Molecular evolution","level":4,"score":0.35249999165534973},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.33970001339912415},{"id":"https://openalex.org/C2992240565","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Protein evolution","level":3,"score":0.33009999990463257},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.30329999327659607},{"id":"https://openalex.org/C120936955","wikidata":"https://www.wikidata.org/wiki/Q2155640","display_name":"Empirical research","level":2,"score":0.30309998989105225},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.29649999737739563},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.2946999967098236},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28630000352859497},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.28290000557899475},{"id":"https://openalex.org/C138025448","wikidata":"https://www.wikidata.org/wiki/Q7662597","display_name":"Synonymous substitution","level":5,"score":0.2806999981403351},{"id":"https://openalex.org/C137583809","wikidata":"https://www.wikidata.org/wiki/Q1096404","display_name":"Modern evolutionary synthesis","level":2,"score":0.27000001072883606}],"mesh":[{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/database/baaf052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaf052","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaf052/64394797/baaf052.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:40996708","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40996708","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:11270883","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12462380","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12462380","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12462380/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"},{"id":"pmh:oai:www.investigo.biblioteca.uvigo.es:11093/10112","is_oa":true,"landing_page_url":"http://hdl.handle.net/11093/10112","pdf_url":null,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/database/baaf052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baaf052","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baaf052/64394797/baaf052.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2017017573","display_name":null,"funder_award_id":"PID2023-151032NB-C22","funder_id":"https://openalex.org/F4320308798","funder_display_name":"Albert Ellis Institute"},{"id":"https://openalex.org/G3480869486","display_name":null,"funder_award_id":"13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G4401187822","display_name":null,"funder_award_id":"REC-SALAS-22","funder_id":"https://openalex.org/F4320321595","funder_display_name":"Federaci\u00f3n Espa\u00f1ola de Enfermedades Raras"},{"id":"https://openalex.org/G7084143925","display_name":null,"funder_award_id":"AEI/10","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320308798","display_name":"Albert Ellis Institute","ror":"https://ror.org/0027wxf59"},{"id":"https://openalex.org/F4320321595","display_name":"Federaci\u00f3n Espa\u00f1ola de Enfermedades Raras","ror":"https://ror.org/0348bpk17"},{"id":"https://openalex.org/F4320324091","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null},{"id":"https://openalex.org/F6553983313","display_name":"Consorcio Interuniversitario do Sistema Universitario de Galicia","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414493548.pdf","grobid_xml":"https://content.openalex.org/works/W4414493548.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W638482479","https://openalex.org/W1492846538","https://openalex.org/W1788771833","https://openalex.org/W1973101413","https://openalex.org/W1984237696","https://openalex.org/W1986759708","https://openalex.org/W1991804333","https://openalex.org/W2011240878","https://openalex.org/W2016811301","https://openalex.org/W2017519756","https://openalex.org/W2021415417","https://openalex.org/W2031700956","https://openalex.org/W2062018285","https://openalex.org/W2068745373","https://openalex.org/W2086558360","https://openalex.org/W2096702350","https://openalex.org/W2097706568","https://openalex.org/W2110335151","https://openalex.org/W2117059491","https://openalex.org/W2119632499","https://openalex.org/W2136847298","https://openalex.org/W2139058004","https://openalex.org/W2139134537","https://openalex.org/W2139310526","https://openalex.org/W2149290147","https://openalex.org/W2152580039","https://openalex.org/W2155196220","https://openalex.org/W2159927403","https://openalex.org/W2162473374","https://openalex.org/W2186750819","https://openalex.org/W2265443415","https://openalex.org/W2327660108","https://openalex.org/W2563535234","https://openalex.org/W2614081736","https://openalex.org/W2778423532","https://openalex.org/W2897701522","https://openalex.org/W2915395120","https://openalex.org/W2949867654","https://openalex.org/W2969866109","https://openalex.org/W2994301183","https://openalex.org/W3012182955","https://openalex.org/W3037064900","https://openalex.org/W3087512677","https://openalex.org/W3131548182","https://openalex.org/W3196647967","https://openalex.org/W4200218518","https://openalex.org/W4205983237","https://openalex.org/W4220833641","https://openalex.org/W4230357098","https://openalex.org/W4283803957","https://openalex.org/W4323040519","https://openalex.org/W4390029161","https://openalex.org/W4392533279","https://openalex.org/W4405670661","https://openalex.org/W4409307277","https://openalex.org/W4409733035"],"related_works":[],"abstract_inverted_index":{"Substitution":[0],"models":[1,32,39,64,83,110,155,178,199,227],"of":[2,8,21,30,59,65,81,98,107,111,158,165,202,206],"protein":[3,26,66,112,117,237],"evolution":[4,67,113,238],"describe":[5],"the":[6,25,56,95,121,159,196,203,207],"patterns":[7],"amino":[9,166,170],"acid":[10,167],"substitutions":[11],"over":[12],"evolutionary":[13,191,230],"time":[14],"and":[15,78,127,143,169,211],"are":[16,33,40],"fundamental":[17],"for":[18,115,235,240],"probabilistic":[19,116],"methods":[20],"phylogenetic":[22,85],"inference.":[23],"At":[24],"level,":[27],"a":[28,53,72,105,136],"variety":[29],"substitution":[31,38,63,100,109,154,168,177,198,226],"available,":[34],"but":[35],"only":[36],"empirical":[37,62,99,108,153,197],"well":[41],"established":[42],"in":[43,141,156,183,200],"phylogenetics":[44,118],"due":[45],"to":[46,186,221],"their":[47,51,162],"mathematical":[48],"simplicity.":[49],"Despite":[50],"importance,":[52],"database":[54,106,132],"compiling":[55],"large":[57],"number":[58],"currently":[60],"available":[61],"is":[68,89,133],"lacking,":[69],"although":[70],"such":[71],"resource":[73],"could":[74],"facilitate":[75],"access,":[76],"assessment,":[77],"subsequent":[79],"implementation":[80],"these":[82],"into":[84,135],"frameworks.":[86],"Besides,":[87],"little":[88],"known":[90],"about":[91],"formal":[92],"comparisons":[93],"between":[94,161],"current":[96],"set":[97],"models.":[101],"We":[102,149,174],"present":[103],"EModelDB,":[104],"required":[114],"that":[119,145,176,213,225],"includes":[120],"corresponding":[122],"exchangeability":[123],"matrices,":[124],"model":[125],"classification,":[126],"model-specific":[128],"biological":[129],"information.":[130],"The":[131],"integrated":[134],"graphical":[137],"user":[138],"interface,":[139],"written":[140],"Python":[142],"SQL,":[144],"facilitates":[146],"its":[147],"usability.":[148],"also":[150],"compared":[151,220],"common":[152],"terms":[157,201],"distance":[160],"relative":[163],"rates":[164],"frequencies":[171],"at":[172],"equilibrium.":[173],"found":[175,212],"derived":[179,208],"from":[180],"proteins":[181,210,219],"related":[182],"nature":[184],"tend":[185],"cluster":[187],"together,":[188],"reflecting":[189],"similar":[190],"patterns.":[192],"Indeed,":[193],"we":[194],"evaluated":[195],"folding":[204,241],"stability":[205],"modeled":[209],"they":[214],"generally":[215],"produce":[216],"less":[217],"stable":[218],"real":[222],"proteins,":[223],"suggesting":[224],"with":[228],"additional":[229],"constraints":[231],"can":[232],"be":[233],"preferred":[234],"studying":[236],"accounting":[239],"stability.":[242],"Database":[243],"URL:":[244],"https://github.com/Paula-Iglesias-Rivas/EModelDB.":[245]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
