{"id":"https://openalex.org/W1998271648","doi":"https://doi.org/10.1186/1471-2105-15-s12-s2","title":"Discovering co-occurring patterns and their biological significance in protein families","display_name":"Discovering co-occurring patterns and their biological significance in protein families","publication_year":2014,"publication_date":"2014-11-06","ids":{"openalex":"https://openalex.org/W1998271648","doi":"https://doi.org/10.1186/1471-2105-15-s12-s2","mag":"1998271648","pmid":"https://pubmed.ncbi.nlm.nih.gov/25474736"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-s12-s2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s12-s2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S12-S2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S12-S2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054354683","display_name":"En-Shiun Annie Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I151746483","display_name":"University of Waterloo","ror":"https://ror.org/01aff2v68","country_code":"CA","type":"education","lineage":["https://openalex.org/I151746483"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"En-Shiun Annie Lee","raw_affiliation_strings":["Department of Systems Design Engineering, University of Waterloo, N2L 3G1, Waterloo, Canada","Department of Systems Design Engineering, University of Waterloo, Waterloo, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Design Engineering, University of Waterloo, N2L 3G1, Waterloo, Canada","institution_ids":["https://openalex.org/I151746483"]},{"raw_affiliation_string":"Department of Systems Design Engineering, University of Waterloo, Waterloo, Canada","institution_ids":["https://openalex.org/I151746483"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067575670","display_name":"Sanderz Fung","orcid":null},"institutions":[{"id":"https://openalex.org/I151746483","display_name":"University of Waterloo","ror":"https://ror.org/01aff2v68","country_code":"CA","type":"education","lineage":["https://openalex.org/I151746483"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Sanderz Fung","raw_affiliation_strings":["Department of Systems Design Engineering, University of Waterloo, N2L 3G1, Waterloo, Canada","Department of Systems Design Engineering, University of Waterloo, Waterloo, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Design Engineering, University of Waterloo, N2L 3G1, Waterloo, Canada","institution_ids":["https://openalex.org/I151746483"]},{"raw_affiliation_string":"Department of Systems Design Engineering, University of Waterloo, Waterloo, Canada","institution_ids":["https://openalex.org/I151746483"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085562456","display_name":"Ho-Yin Sze-To","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ho-Yin Sze-To","raw_affiliation_strings":["Computer Science and Engineering, Chinese University of Hong Kong, Shatin, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Engineering, Chinese University of Hong Kong, Shatin, Hong Kong, China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051841038","display_name":"Andrew K. C. Wong","orcid":"https://orcid.org/0000-0002-0019-7152"},"institutions":[{"id":"https://openalex.org/I151746483","display_name":"University of Waterloo","ror":"https://ror.org/01aff2v68","country_code":"CA","type":"education","lineage":["https://openalex.org/I151746483"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Andrew K C Wong","raw_affiliation_strings":["Department of Systems Design Engineering, University of Waterloo, N2L 3G1, Waterloo, Canada","Department of Systems Design Engineering, University of Waterloo, Waterloo, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Design Engineering, University of Waterloo, N2L 3G1, Waterloo, Canada","institution_ids":["https://openalex.org/I151746483"]},{"raw_affiliation_string":"Department of Systems Design Engineering, University of Waterloo, Waterloo, Canada","institution_ids":["https://openalex.org/I151746483"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5054354683"],"corresponding_institution_ids":["https://openalex.org/I151746483"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.7114,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.69310658,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"15","issue":"S12","first_page":"S2","last_page":"S2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.15479999780654907,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.15479999780654907,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.15080000460147858,"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":0.10830000042915344,"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/amino-acid","display_name":"Amino acid","score":0.7109023332595825},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5653802752494812},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.5529308319091797},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49415257573127747},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.4634200632572174},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4579467177391052},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.456348717212677},{"id":"https://openalex.org/keywords/closeness","display_name":"Closeness","score":0.45532017946243286},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4492170810699463},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.41464120149612427},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.413472056388855},{"id":"https://openalex.org/keywords/taxonomic-rank","display_name":"Taxonomic rank","score":0.4114115238189697},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.36785799264907837},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.33039146661758423},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1630435585975647},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.09338989853858948}],"concepts":[{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.7109023332595825},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5653802752494812},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.5529308319091797},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49415257573127747},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.4634200632572174},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4579467177391052},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.456348717212677},{"id":"https://openalex.org/C2779545769","wikidata":"https://www.wikidata.org/wiki/Q5135364","display_name":"Closeness","level":2,"score":0.45532017946243286},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4492170810699463},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.41464120149612427},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.413472056388855},{"id":"https://openalex.org/C189592816","wikidata":"https://www.wikidata.org/wiki/Q427626","display_name":"Taxonomic rank","level":3,"score":0.4114115238189697},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.36785799264907837},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.33039146661758423},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1630435585975647},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.09338989853858948},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025801","descriptor_name":"Ubiquitin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D025801","descriptor_name":"Ubiquitin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D025801","descriptor_name":"Ubiquitin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D045304","descriptor_name":"Cytochromes c","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D045304","descriptor_name":"Cytochromes c","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D045304","descriptor_name":"Cytochromes c","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-15-s12-s2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s12-s2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S12-S2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25474736","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25474736","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4243116","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4243116","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-s12-s2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-s12-s2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S12-S2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.5799999833106995,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1998271648.pdf","grobid_xml":"https://content.openalex.org/works/W1998271648.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W345458310","https://openalex.org/W1535002880","https://openalex.org/W1565377632","https://openalex.org/W1663973292","https://openalex.org/W1960714090","https://openalex.org/W1978046058","https://openalex.org/W1979762151","https://openalex.org/W1981024715","https://openalex.org/W1985912243","https://openalex.org/W2000137866","https://openalex.org/W2001626642","https://openalex.org/W2002638840","https://openalex.org/W2008545402","https://openalex.org/W2009086942","https://openalex.org/W2011430131","https://openalex.org/W2020899421","https://openalex.org/W2031764760","https://openalex.org/W2038744179","https://openalex.org/W2039213651","https://openalex.org/W2040890941","https://openalex.org/W2049914596","https://openalex.org/W2050367448","https://openalex.org/W2051664277","https://openalex.org/W2055390996","https://openalex.org/W2058968319","https://openalex.org/W2067271823","https://openalex.org/W2073459772","https://openalex.org/W2085517529","https://openalex.org/W2092672051","https://openalex.org/W2106882534","https://openalex.org/W2113358325","https://openalex.org/W2130468514","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2132914434","https://openalex.org/W2137991504","https://openalex.org/W2141885858","https://openalex.org/W2143701918","https://openalex.org/W2144362290","https://openalex.org/W2162992520","https://openalex.org/W2166594637","https://openalex.org/W2170181608","https://openalex.org/W2417996941","https://openalex.org/W2482589566","https://openalex.org/W2605068739","https://openalex.org/W4210623056","https://openalex.org/W4240197696"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W2181549235","https://openalex.org/W2003319012","https://openalex.org/W2026660542","https://openalex.org/W1968549100","https://openalex.org/W2804480386","https://openalex.org/W3186624150","https://openalex.org/W65850283"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,68],"large":[2],"influx":[3],"of":[4,10,71,75,88,197,214,249,269],"biological":[5,22,69,93,207],"sequences":[6,18,46],"poses":[7],"the":[8,44,72,92,147,179,194,198,201,210,215,218,223,242,253,261,267,270,294,327],"importance":[9],"identifying":[11],"and":[12,91,121,137,200,233,257,283,307],"correlating":[13],"conserved":[14,25,39,57,76,131,285],"regions":[15,26,40,58,77,98,132,286],"in":[16,59,96,241,252,260,311,319],"homologous":[17],"to":[19,49,130,164,247,266,303,331],"acquire":[20],"valuable":[21],"knowledge.":[23],"These":[24,313],"contain":[27,288],"statistically":[28,110],"significant":[29,111,301],"residue":[30],"associations":[31,114],"as":[32,99,115,165,229,231,322],"sequence":[33,116],"patterns.":[34,117],"Thus,":[35,275],"patterns":[36,65,80,289,298],"from":[37],"two":[38,148],"co-occurring":[41,292],"frequently":[42,142,291],"on":[43,293],"same":[45,219,295],"are":[47,225,299],"inferred":[48],"have":[50,150],"joint":[51],"functionality.":[52],"A":[53],"method":[54],"for":[55,176,227,329],"finding":[56],"protein":[60],"families":[61],"with":[62,78,133,144,157],"frequent":[63],"co-occurrence":[64,159,244,263,277],"is":[66,186],"proposed.":[67],"significance":[70,208],"discovered":[73,109],"clusters":[74],"co-occurrences":[79],"can":[81,280,324],"be":[82],"validated":[83],"by":[84,101],"their":[85,183,304],"three-dimensional":[86,180,305],"closeness":[87,306],"amino":[89,112,134,184,190,212,239,258],"acids":[90,185,213,240,259],"functionality":[94],"found":[95],"those":[97],"supported":[100],"published":[102],"work.":[103],"METHODS:":[104],"Using":[105],"existing":[106],"algorithms,":[107],"we":[108,162,205],"acid":[113,135,191],"We":[118,153],"then":[119,154],"aligned":[120],"clustered":[122,155],"them":[123],"into":[124,160],"Aligned":[125],"Pattern":[126],"Clusters":[127,168,196],"(APCs)":[128],"corresponding":[129],"conservation":[136],"variation.":[138],"When":[139],"one":[140],"APC":[141,167],"co-occurred":[143],"another":[145],"APC,":[146],"APCs":[149,156,216],"high":[151,158],"co-occurrence.":[152],"what":[161],"refer":[163],"Co-occurrence":[166,177,195],"(Co-occurrence":[169],"Clusters).":[170],"RESULTS:":[171],"Our":[172],"results":[173,314],"show":[174],"that":[175,287,290],"Clusters,":[178],"distance":[181],"between":[182],"closer":[187],"than":[188],"average":[189],"distances.":[192],"For":[193],"ubiquitin":[199],"cytochrome":[202,237],"c":[203],"families,":[204],"observed":[206],"among":[209],"residing":[211],"within":[217],"cluster.":[220],"In":[221,236],"ubiquitin,":[222],"residues":[224],"responsible":[226],"ubiquitination":[228],"well":[230],"conventional":[232],"unconventional":[234],"ubiquitin-bindings.":[235],"c,":[238],"first":[243],"cluster":[245,264],"contribute":[246,265],"binding":[248],"other":[250,308],"proteins":[251],"electron":[254],"transport":[255],"chain,":[256],"second":[262],"stability":[268],"axial":[271],"heme":[272],"ligand.":[273],"CONCLUSIONS:":[274],"our":[276],"clustering":[278],"algorithm":[279],"efficiently":[281],"find":[282],"rank":[284],"proteins.":[296],"Co-occurring":[297],"biologically":[300],"due":[302],"evidences":[309],"reported":[310],"literature.":[312],"play":[315],"an":[316],"important":[317],"role":[318],"drug":[320],"discovery":[321],"biologists":[323],"quickly":[325],"identify":[326],"target":[328],"drugs":[330],"conduct":[332],"detailed":[333],"preclinical":[334],"studies.":[335]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
