{"id":"https://openalex.org/W2074706385","doi":"https://doi.org/10.1371/journal.pcbi.1000867","title":"More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology","display_name":"More Than 1,001 Problems with Protein Domain Databases: Transmembrane Regions, Signal Peptides and the Issue of Sequence Homology","publication_year":2010,"publication_date":"2010-07-29","ids":{"openalex":"https://openalex.org/W2074706385","doi":"https://doi.org/10.1371/journal.pcbi.1000867","mag":"2074706385","pmid":"https://pubmed.ncbi.nlm.nih.gov/20686689"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1000867","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000867","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000867&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.1000867&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026949619","display_name":"Wing\u2010Cheong Wong","orcid":"https://orcid.org/0000-0003-1247-6279"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Wing-Cheong Wong","raw_affiliation_strings":["Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore. wongwc@bii-sg.org","Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore. wongwc@bii-sg.org","institution_ids":["https://openalex.org/I115228651"]},{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019975803","display_name":"Sebastian Maurer\u2010Stroh","orcid":"https://orcid.org/0000-0003-0813-9640"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Sebastian Maurer-Stroh","raw_affiliation_strings":["Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore","School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore","School of Biological Sciences (SBS), Nanyang Technological University (NTU), , Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]},{"raw_affiliation_string":"School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Biological Sciences (SBS), Nanyang Technological University (NTU), , Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007579711","display_name":"Frank Eisenhaber","orcid":"https://orcid.org/0000-0002-9599-5420"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I4210148498","display_name":"Bioinformatics Institute","ror":"https://ror.org/044w3nw43","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2801752549","https://openalex.org/I4210148498"]},{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Frank Eisenhaber","raw_affiliation_strings":["Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore","Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore","School of Computer Engineering (SCE), Nanyang Technological University (NTU), Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I4210148498"]},{"raw_affiliation_string":"Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"School of Computer Engineering (SCE), Nanyang Technological University (NTU), Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5007579711","https://openalex.org/A5019975803","https://openalex.org/A5026949619"],"corresponding_institution_ids":["https://openalex.org/I115228651","https://openalex.org/I165932596","https://openalex.org/I172675005","https://openalex.org/I4210148498"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.858,"has_fulltext":true,"cited_by_count":60,"citation_normalized_percentile":{"value":0.90883633,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"6","issue":"7","first_page":"e1000867","last_page":"e1000867"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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/T12254","display_name":"Machine Learning in Bioinformatics","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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9987999796867371,"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/computational-biology","display_name":"Computational biology","score":0.5857212543487549},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.530159056186676},{"id":"https://openalex.org/keywords/transmembrane-domain","display_name":"Transmembrane domain","score":0.5169493556022644},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.5040985345840454},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.47300034761428833},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4614364802837372},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4556051790714264},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.4528745412826538},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.43859028816223145},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.43825945258140564},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.42703989148139954},{"id":"https://openalex.org/keywords/loop-modeling","display_name":"Loop modeling","score":0.4134834110736847},{"id":"https://openalex.org/keywords/transmembrane-protein","display_name":"Transmembrane protein","score":0.4130139946937561},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3667224049568176},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.3422219753265381},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.30547431111335754},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22172653675079346},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13728073239326477},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1050245463848114}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5857212543487549},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.530159056186676},{"id":"https://openalex.org/C118892022","wikidata":"https://www.wikidata.org/wiki/Q7834587","display_name":"Transmembrane domain","level":3,"score":0.5169493556022644},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.5040985345840454},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.47300034761428833},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4614364802837372},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4556051790714264},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.4528745412826538},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.43859028816223145},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.43825945258140564},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.42703989148139954},{"id":"https://openalex.org/C45475804","wikidata":"https://www.wikidata.org/wiki/Q6675846","display_name":"Loop modeling","level":4,"score":0.4134834110736847},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.4130139946937561},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3667224049568176},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3422219753265381},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.30547431111335754},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22172653675079346},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13728073239326477},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1050245463848114},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","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":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","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":"D021382","descriptor_name":"Protein Sorting Signals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021382","descriptor_name":"Protein Sorting Signals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021382","descriptor_name":"Protein Sorting Signals","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":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1000867","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000867","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000867&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:20686689","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20686689","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:scholarbank.nus.edu.sg:10635/165418","is_oa":false,"landing_page_url":"https://scholarbank.nus.edu.sg/handle/10635/165418","pdf_url":null,"source":{"id":"https://openalex.org/S7407052290","display_name":"National University of Singapore","issn_l":null,"issn":[],"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Unpaywall 20200320","raw_type":"Article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1000867","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000867","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:976be14b0b914c68b23ca1445a95f92e","is_oa":true,"landing_page_url":"https://doaj.org/article/976be14b0b914c68b23ca1445a95f92e","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 6, Iss 7, p e1000867 (2010)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/142479","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/More_Than_1_001_Problems_with_Protein_Domain_Databases_Transmembrane_Regions_Signal_Peptides_and_the_Issue_of_Sequence_Homology/142479","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:2912341","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2912341","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.1000867","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1000867","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000867&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":[{"score":0.47999998927116394,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2074706385.pdf","grobid_xml":"https://content.openalex.org/works/W2074706385.grobid-xml"},"referenced_works_count":128,"referenced_works":["https://openalex.org/W154993808","https://openalex.org/W204050705","https://openalex.org/W1484097762","https://openalex.org/W1489167250","https://openalex.org/W1513332069","https://openalex.org/W1513939725","https://openalex.org/W1522556730","https://openalex.org/W1596520144","https://openalex.org/W1645373081","https://openalex.org/W1740355754","https://openalex.org/W1774728382","https://openalex.org/W1854397683","https://openalex.org/W1865931858","https://openalex.org/W1868379549","https://openalex.org/W1965266514","https://openalex.org/W1967850886","https://openalex.org/W1971147414","https://openalex.org/W1972918915","https://openalex.org/W1977922844","https://openalex.org/W1978585427","https://openalex.org/W1979845325","https://openalex.org/W1979880724","https://openalex.org/W1992596028","https://openalex.org/W1992721181","https://openalex.org/W1995053766","https://openalex.org/W1996112765","https://openalex.org/W1996351562","https://openalex.org/W2003706919","https://openalex.org/W2003788979","https://openalex.org/W2008116827","https://openalex.org/W2008399824","https://openalex.org/W2009570821","https://openalex.org/W2014719716","https://openalex.org/W2015546050","https://openalex.org/W2019345165","https://openalex.org/W2028717023","https://openalex.org/W2031903428","https://openalex.org/W2034911186","https://openalex.org/W2035333716","https://openalex.org/W2036792999","https://openalex.org/W2039330662","https://openalex.org/W2041266066","https://openalex.org/W2042540642","https://openalex.org/W2049355199","https://openalex.org/W2050067275","https://openalex.org/W2060286193","https://openalex.org/W2060797027","https://openalex.org/W2067070171","https://openalex.org/W2068018119","https://openalex.org/W2068770352","https://openalex.org/W2070402073","https://openalex.org/W2071392219","https://openalex.org/W2076260974","https://openalex.org/W2082418604","https://openalex.org/W2085277871","https://openalex.org/W2086586192","https://openalex.org/W2090866092","https://openalex.org/W2091283864","https://openalex.org/W2093377893","https://openalex.org/W2094766468","https://openalex.org/W2095392992","https://openalex.org/W2096503271","https://openalex.org/W2099182237","https://openalex.org/W2099254366","https://openalex.org/W2100018338","https://openalex.org/W2101783948","https://openalex.org/W2102771044","https://openalex.org/W2102856132","https://openalex.org/W2103461849","https://openalex.org/W2107251251","https://openalex.org/W2107757325","https://openalex.org/W2110498021","https://openalex.org/W2112620326","https://openalex.org/W2114083522","https://openalex.org/W2117813757","https://openalex.org/W2119537921","https://openalex.org/W2119910427","https://openalex.org/W2121520117","https://openalex.org/W2122281839","https://openalex.org/W2123858481","https://openalex.org/W2124088653","https://openalex.org/W2124871329","https://openalex.org/W2126578619","https://openalex.org/W2128549389","https://openalex.org/W2128653811","https://openalex.org/W2131794450","https://openalex.org/W2133312664","https://openalex.org/W2133787379","https://openalex.org/W2136767810","https://openalex.org/W2139621307","https://openalex.org/W2141011718","https://openalex.org/W2141885858","https://openalex.org/W2141941210","https://openalex.org/W2143210482","https://openalex.org/W2143599839","https://openalex.org/W2144540541","https://openalex.org/W2144944670","https://openalex.org/W2147295137","https://openalex.org/W2147562836","https://openalex.org/W2147898421","https://openalex.org/W2148311769","https://openalex.org/W2148386309","https://openalex.org/W2148622452","https://openalex.org/W2150999244","https://openalex.org/W2151034762","https://openalex.org/W2151823434","https://openalex.org/W2153180326","https://openalex.org/W2154205489","https://openalex.org/W2154902969","https://openalex.org/W2156125289","https://openalex.org/W2158714788","https://openalex.org/W2158906453","https://openalex.org/W2159559878","https://openalex.org/W2161746138","https://openalex.org/W2163105490","https://openalex.org/W2163895365","https://openalex.org/W2168223461","https://openalex.org/W2344156640","https://openalex.org/W2991631909","https://openalex.org/W3214380909","https://openalex.org/W4210623056","https://openalex.org/W4229954146","https://openalex.org/W4245668478","https://openalex.org/W4252166161","https://openalex.org/W4293014210","https://openalex.org/W6631117463","https://openalex.org/W6926829796","https://openalex.org/W7026854212"],"related_works":["https://openalex.org/W3204091482","https://openalex.org/W10948732","https://openalex.org/W1978088031","https://openalex.org/W2161896699","https://openalex.org/W2059079931","https://openalex.org/W2157930580","https://openalex.org/W1595347157","https://openalex.org/W2406523068","https://openalex.org/W2140187548","https://openalex.org/W2121560377"],"abstract_inverted_index":{"Large-scale":[0],"genome":[1],"sequencing":[2],"gained":[3],"general":[4],"importance":[5],"for":[6,91,244,294],"life":[7],"science":[8],"because":[9],"functional":[10],"annotation":[11,263,298],"of":[12,23,30,32,46,65,70,100,115,124,129,135,154,161,166,198,237,247,286],"otherwise":[13],"experimentally":[14],"uncharacterized":[15],"sequences":[16,34],"is":[17,111],"made":[18],"possible":[19],"by":[20,214,256,297],"the":[21,28,50,57,60,82,98,127,151,182,196,210,216,220,266,273,278],"theory":[22],"biomolecular":[24],"sequence":[25,71,109],"homology.":[26],"Historically,":[27],"paradigm":[29],"similarity":[31,64,72,110],"protein":[33,75],"implying":[35],"common":[36,120,271],"structure,":[37],"function":[38],"and":[39,104,158,235],"ancestry":[40],"was":[41],"generalized":[42],"based":[43],"on":[44],"studies":[45],"globular":[47],"domains.":[48],"Having":[49],"same":[51,83],"fold":[52],"imposes":[53],"strict":[54],"conditions":[55],"over":[56],"packing":[58],"in":[59,97,203,270],"hydrophobic":[61,66,131,217],"core":[62],"requiring":[63],"patterns.":[67],"The":[68],"implications":[69],"among":[73,150,185],"non-globular":[74],"segments":[76],"have":[77],"not":[78],"been":[79],"studied":[80],"to":[81,143,180,261],"extent;":[84],"nevertheless,":[85],"homology":[86],"considerations":[87],"are":[88],"silently":[89],"extended":[90],"them.":[92],"This":[93],"appears":[94],"especially":[95],"detrimental":[96],"case":[99],"transmembrane":[101],"helices":[102],"(TMs)":[103],"signal":[105],"peptides":[106],"(SPs)":[107],"where":[108,265],"necessarily":[112],"a":[113,245,284],"consequence":[114],"physical":[116],"requirements":[117],"rather":[118],"than":[119,147],"ancestry.":[121],"Thus,":[122,251],"matching":[123,130,215],"SPs/TMs":[125,136],"creates":[126],"illusion":[128],"cores.":[132],"Therefore,":[133],"inclusion":[134],"into":[137,209],"domain":[138,249,253,275],"models":[139,153,293],"can":[140,206,259],"give":[141],"rise":[142],"wrong":[144],"annotations.":[145],"More":[146,189],"1001":[148],"domains":[149,160],"10,340":[152],"Pfam":[155,240],"release":[156],"23":[157],"18":[159],"SMART":[162],"version":[163],"6":[164],"(out":[165],"809)":[167],"contain":[168],"SP/TM":[169,183,257,279],"regions.":[170],"As":[171],"expected,":[172],"fragment-mode":[173],"HMM":[174],"searches":[175],"generate":[176],"promiscuous":[177],"hits":[178,241,254,289],"limited":[179],"solely":[181],"part":[184],"clearly":[186,199],"unrelated":[187],"proteins.":[188],"worryingly,":[190],"we":[191,228],"show":[192],"explicit":[193],"examples":[194],"that":[195,230],"scores":[197],"false-positive":[200,252],"hits,":[201],"even":[202],"global-mode":[204],"searches,":[205],"be":[207],"elevated":[208],"significance":[211],"range":[212],"just":[213],"runs.":[218],"In":[219],"PIR":[221],"iProClass":[222],"database":[223],"v3.74":[224],"using":[225],"conservative":[226],"criteria,":[227],"find":[229],"at":[231],"least":[232],"between":[233],"2.1%":[234],"13.6%":[236],"its":[238],"annotated":[239],"appear":[242],"unjustified":[243],"set":[246],"validated":[248],"models.":[250],"enforced":[255],"regions":[258],"lead":[260],"dramatic":[262],"errors":[264],"hit":[267],"has":[268],"nothing":[269],"with":[272],"problematic":[274,288],"model":[276],"except":[277],"region":[280],"itself.":[281],"We":[282],"suggest":[283],"workflow":[285],"flagging":[287],"arising":[290],"from":[291],"SP/TM-containing":[292],"critical":[295],"reconsideration":[296],"users.":[299]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":8}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}