{"id":"https://openalex.org/W1965827393","doi":"https://doi.org/10.1371/journal.pcbi.1003926","title":"ECOD: An Evolutionary Classification of Protein Domains","display_name":"ECOD: An Evolutionary Classification of Protein Domains","publication_year":2014,"publication_date":"2014-12-04","ids":{"openalex":"https://openalex.org/W1965827393","doi":"https://doi.org/10.1371/journal.pcbi.1003926","mag":"1965827393","pmid":"https://pubmed.ncbi.nlm.nih.gov/25474468"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003926","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003926","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003926&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003926&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014351098","display_name":"Hua Cheng","orcid":"https://orcid.org/0000-0002-0079-8820"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hua Cheng","raw_affiliation_strings":["Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I4210096815","https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025471816","display_name":"R. Dustin Schaeffer","orcid":"https://orcid.org/0000-0001-6502-1425"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. Dustin Schaeffer","raw_affiliation_strings":["Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I4210096815","https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061738557","display_name":"Yuxing Liao","orcid":"https://orcid.org/0000-0002-1238-2021"},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuxing Liao","raw_affiliation_strings":["Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048271521","display_name":"Lisa N. Kinch","orcid":"https://orcid.org/0000-0003-3041-2615"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lisa N. Kinch","raw_affiliation_strings":["Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I4210096815","https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037320644","display_name":"Jimin Pei","orcid":"https://orcid.org/0000-0002-3505-9665"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jimin Pei","raw_affiliation_strings":["Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I4210096815","https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000265011","display_name":"Shuoyong Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuoyong Shi","raw_affiliation_strings":["Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109920124","display_name":"Bong-Hyun Kim","orcid":null},"institutions":[{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bong-Hyun Kim","raw_affiliation_strings":["Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108096094","display_name":"Nick V. Grishin","orcid":null},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I4210096815","display_name":"Southwestern Medical Center","ror":"https://ror.org/00t9vx427","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210096815"]},{"id":"https://openalex.org/I867280407","display_name":"The University of Texas Southwestern Medical Center","ror":"https://ror.org/05byvp690","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I867280407"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nick V. Grishin","raw_affiliation_strings":["Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America; Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America; Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I867280407"]},{"raw_affiliation_string":"Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I4210096815","https://openalex.org/I867280407"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5108096094"],"corresponding_institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I4210096815","https://openalex.org/I867280407"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":6.5002,"has_fulltext":true,"cited_by_count":485,"citation_normalized_percentile":{"value":0.97610847,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"10","issue":"12","first_page":"e1003926","last_page":"e1003926"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9969000220298767,"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":0.9969000220298767,"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":0.9955000281333923,"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":0.9937999844551086,"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/protein-superfamily","display_name":"Protein superfamily","score":0.7294349074363708},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.6867107152938843},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.6844199895858765},{"id":"https://openalex.org/keywords/structural-classification-of-proteins-database","display_name":"Structural Classification of Proteins database","score":0.6724144816398621},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.5669021606445312},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.5320321917533875},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47724151611328125},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.4771670401096344},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4734365940093994},{"id":"https://openalex.org/keywords/sequence-homology","display_name":"Sequence homology","score":0.46902337670326233},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.45465540885925293},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.4487352967262268},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.44685134291648865},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4301571846008301},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.41420426964759827},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4140656590461731},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.297011137008667},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.22435584664344788},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19388622045516968}],"concepts":[{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.7294349074363708},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.6867107152938843},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.6844199895858765},{"id":"https://openalex.org/C58773245","wikidata":"https://www.wikidata.org/wiki/Q4832556","display_name":"Structural Classification of Proteins database","level":3,"score":0.6724144816398621},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.5669021606445312},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.5320321917533875},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47724151611328125},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.4771670401096344},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4734365940093994},{"id":"https://openalex.org/C2779315201","wikidata":"https://www.wikidata.org/wiki/Q414601","display_name":"Sequence homology","level":4,"score":0.46902337670326233},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.45465540885925293},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.4487352967262268},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.44685134291648865},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4301571846008301},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.41420426964759827},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4140656590461731},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.297011137008667},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.22435584664344788},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19388622045516968},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","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":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1003926","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003926","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003926&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmid:25474468","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25474468","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:e69bf408313645bb90454b2e05f85df3","is_oa":true,"landing_page_url":"https://doaj.org/article/e69bf408313645bb90454b2e05f85df3","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 10, Iss 12, p e1003926 (2014)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4256011","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4256011","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003926","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003926","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003926&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1023413749","display_name":null,"funder_award_id":"I-505","funder_id":"https://openalex.org/F4320306196","funder_display_name":"Welch Foundation"},{"id":"https://openalex.org/G3368261749","display_name":null,"funder_award_id":"R01 GM094575","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G571576816","display_name":null,"funder_award_id":"GM094575","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G834155436","display_name":null,"funder_award_id":"GM-094575","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306082","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90"},{"id":"https://openalex.org/F4320306196","display_name":"Welch Foundation","ror":"https://ror.org/00np6vq88"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1965827393.pdf","grobid_xml":"https://content.openalex.org/works/W1965827393.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W1783714080","https://openalex.org/W1956332901","https://openalex.org/W1976558061","https://openalex.org/W1977949834","https://openalex.org/W1994128537","https://openalex.org/W1997806799","https://openalex.org/W1997817672","https://openalex.org/W1997850393","https://openalex.org/W2000118138","https://openalex.org/W2001600076","https://openalex.org/W2003672142","https://openalex.org/W2005795025","https://openalex.org/W2013404472","https://openalex.org/W2019240387","https://openalex.org/W2022058405","https://openalex.org/W2023790301","https://openalex.org/W2026097376","https://openalex.org/W2026948008","https://openalex.org/W2032293502","https://openalex.org/W2037993016","https://openalex.org/W2048457764","https://openalex.org/W2055631962","https://openalex.org/W2057272352","https://openalex.org/W2060791849","https://openalex.org/W2067785100","https://openalex.org/W2082667898","https://openalex.org/W2083988452","https://openalex.org/W2085277871","https://openalex.org/W2088697866","https://openalex.org/W2092162343","https://openalex.org/W2097632784","https://openalex.org/W2100071542","https://openalex.org/W2102245393","https://openalex.org/W2102652793","https://openalex.org/W2108067237","https://openalex.org/W2110397834","https://openalex.org/W2121704271","https://openalex.org/W2124368307","https://openalex.org/W2127194261","https://openalex.org/W2130479394","https://openalex.org/W2130634514","https://openalex.org/W2131410522","https://openalex.org/W2132926880","https://openalex.org/W2133657429","https://openalex.org/W2136116905","https://openalex.org/W2136391678","https://openalex.org/W2138116388","https://openalex.org/W2141885858","https://openalex.org/W2142678478","https://openalex.org/W2145268834","https://openalex.org/W2147739124","https://openalex.org/W2152869198","https://openalex.org/W2154802584","https://openalex.org/W2158714788","https://openalex.org/W2159675211","https://openalex.org/W2161072217","https://openalex.org/W2163940928","https://openalex.org/W2166984808","https://openalex.org/W2337352687","https://openalex.org/W4246643264","https://openalex.org/W4251309463","https://openalex.org/W4320301318"],"related_works":["https://openalex.org/W2075451741","https://openalex.org/W2070693796","https://openalex.org/W2139240863","https://openalex.org/W2164753093","https://openalex.org/W2170171070","https://openalex.org/W4235848672","https://openalex.org/W1997379747","https://openalex.org/W2169356867","https://openalex.org/W4232453105","https://openalex.org/W2106883599"],"abstract_inverted_index":{"Understanding":[0],"the":[1,115,130,140,232],"evolution":[2],"of":[3,37,58,86,90,97,118,133,144,198,223,234],"a":[4,33],"protein,":[5],"including":[6],"both":[7],"close":[8,178],"and":[9,18,21,45,51,112,136,146,193,201,243],"distant":[10,126],"relationships,":[11],"often":[12],"reveals":[13],"insight":[14],"into":[15,172,177],"its":[16],"structure":[17,99],"function.":[19],"Fast":[20],"easy":[22],"access":[23],"to":[24,93,110,139,179,240],"such":[25],"up-to-date":[26],"information":[27],"facilitates":[28],"research.":[29],"We":[30],"have":[31],"developed":[32],"hierarchical":[34],"evolutionary":[35,74,119,181,244],"classification":[36,184],"all":[38,214],"proteins":[39,135,225],"with":[40,208],"experimentally":[41],"determined":[42],"spatial":[43],"structures,":[44],"presented":[46],"it":[47,69],"as":[48,148,150],"an":[49,188],"interactive":[50],"updatable":[52],"online":[53],"database.":[54],"ECOD":[55,101,154,171,212,236],"(Evolutionary":[56],"Classification":[57],"protein":[59,98,161,166,215],"Domains)":[60],"is":[61,185],"distinct":[62],"from":[63],"other":[64,229],"structural":[65,122],"classifications":[66],"in":[67,95,170,228],"that":[68,107,191],"groups":[70],"domains":[71,89],"primarily":[72],"by":[73,187],"relationships":[75,159],"(homology),":[76],"rather":[77],"than":[78],"topology":[79,92],"(or":[80],"\"fold\").":[81],"This":[82,206],"distinction":[83],"highlights":[84],"cases":[85],"homology":[87],"between":[88,160],"differing":[91],"aid":[94],"understanding":[96],"evolution.":[100],"uniquely":[102,210],"emphasizes":[103],"distantly":[104],"related":[105],"homologs":[106,127],"are":[108,168],"difficult":[109],"detect,":[111],"thus":[113],"catalogs":[114],"largest":[116],"number":[117],"links":[120],"among":[121,213],"domain":[123],"classifications.":[124,216],"Placing":[125],"together":[128],"underscores":[129],"ancestral":[131],"similarities":[132],"these":[134],"draws":[137],"attention":[138],"most":[141],"important":[142],"regions":[143],"sequence":[145,174],"structure,":[147],"well":[149],"conserved":[151],"functional":[152],"sites.":[153],"also":[155],"recognizes":[156],"closer":[157],"sequence-based":[158],"domains.":[162],"Currently,":[163],"approximately":[164],"100,000":[165],"structures":[167,200],"classified":[169],"9,000":[173],"families":[175],"clustered":[176],"2,000":[180],"groups.":[182],"The":[183],"assisted":[186],"automated":[189],"pipeline":[190],"quickly":[192],"consistently":[194],"classifies":[195],"weekly":[196],"releases":[197],"PDB":[199,209],"allows":[202],"for":[203],"continual":[204],"updates.":[205],"synchronization":[207],"distinguishes":[211],"Finally,":[217],"we":[218],"present":[219],"several":[220],"case":[221],"studies":[222],"homologous":[224],"not":[226],"recorded":[227],"classifications,":[230],"illustrating":[231],"potential":[233],"how":[235],"can":[237],"be":[238],"used":[239],"further":[241],"biological":[242],"studies.":[245]},"counts_by_year":[{"year":2026,"cited_by_count":27},{"year":2025,"cited_by_count":51},{"year":2024,"cited_by_count":75},{"year":2023,"cited_by_count":57},{"year":2022,"cited_by_count":58},{"year":2021,"cited_by_count":54},{"year":2020,"cited_by_count":40},{"year":2019,"cited_by_count":28},{"year":2018,"cited_by_count":44},{"year":2017,"cited_by_count":22},{"year":2016,"cited_by_count":14},{"year":2015,"cited_by_count":14}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
