{"id":"https://openalex.org/W2568061956","doi":"https://doi.org/10.1093/bioinformatics/btw815","title":"Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function","display_name":"Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function","publication_year":2016,"publication_date":"2016-12-20","ids":{"openalex":"https://openalex.org/W2568061956","doi":"https://doi.org/10.1093/bioinformatics/btw815","mag":"2568061956","pmid":"https://pubmed.ncbi.nlm.nih.gov/28052926"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw815","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw815","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/9/1338/25151227/btw815.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/9/1338/25151227/btw815.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055119846","display_name":"Jeremy Adams","orcid":"https://orcid.org/0000-0003-1215-8123"},"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":"Jeremy Adams","raw_affiliation_strings":["Department of Biology, University of Waterloo, Waterloo, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Waterloo, Waterloo, Ontario, Canada","institution_ids":["https://openalex.org/I151746483"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005067425","display_name":"Michael J. Mansfield","orcid":"https://orcid.org/0000-0003-4717-4721"},"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":"Michael J Mansfield","raw_affiliation_strings":["Department of Biology, University of Waterloo, Waterloo, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Waterloo, Waterloo, Ontario, Canada","institution_ids":["https://openalex.org/I151746483"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079428283","display_name":"Daniel Richard","orcid":"https://orcid.org/0000-0001-8568-9473"},"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":"Daniel J Richard","raw_affiliation_strings":["Department of Biology, University of Waterloo, Waterloo, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Waterloo, Waterloo, Ontario, Canada","institution_ids":["https://openalex.org/I151746483"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032187526","display_name":"Andrew C. Doxey","orcid":"https://orcid.org/0000-0003-2015-099X"},"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":"Andrew C Doxey","raw_affiliation_strings":["Department of Biology, University of Waterloo, Waterloo, Ontario, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Waterloo, Waterloo, Ontario, Canada","institution_ids":["https://openalex.org/I151746483"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5032187526"],"corresponding_institution_ids":["https://openalex.org/I151746483"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.5689,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.84228028,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"33","issue":"9","first_page":"1338","last_page":"1345"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9976000189781189,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9976000189781189,"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":0.9973000288009644,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9921000003814697,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7355802059173584},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6968021392822266},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5821331143379211},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.5715043544769287},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5266808271408081},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5188025832176208},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.5113932490348816},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4821578860282898},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.4493477940559387},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.44124293327331543},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4362945854663849},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2313477098941803},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.12442263960838318}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7355802059173584},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6968021392822266},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5821331143379211},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.5715043544769287},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5266808271408081},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5188025832176208},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5113932490348816},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4821578860282898},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.4493477940559387},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.44124293327331543},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4362945854663849},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2313477098941803},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.12442263960838318},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010944","descriptor_name":"Plants","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btw815","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw815","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/9/1338/25151227/btw815.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28052926","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28052926","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw815","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw815","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/9/1338/25151227/btw815.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2568061956.pdf","grobid_xml":"https://content.openalex.org/works/W2568061956.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W1489145507","https://openalex.org/W1828476563","https://openalex.org/W1956577542","https://openalex.org/W1966503742","https://openalex.org/W1973941375","https://openalex.org/W1976066719","https://openalex.org/W1977278302","https://openalex.org/W1987819535","https://openalex.org/W1996778526","https://openalex.org/W1998808728","https://openalex.org/W2000137866","https://openalex.org/W2000471751","https://openalex.org/W2013863297","https://openalex.org/W2020170893","https://openalex.org/W2024394768","https://openalex.org/W2024620705","https://openalex.org/W2026241873","https://openalex.org/W2028942681","https://openalex.org/W2034758902","https://openalex.org/W2038978937","https://openalex.org/W2043949158","https://openalex.org/W2044044562","https://openalex.org/W2049232195","https://openalex.org/W2058282447","https://openalex.org/W2058320449","https://openalex.org/W2069824853","https://openalex.org/W2073297072","https://openalex.org/W2076617993","https://openalex.org/W2085374743","https://openalex.org/W2097977090","https://openalex.org/W2100301244","https://openalex.org/W2101648814","https://openalex.org/W2103546861","https://openalex.org/W2110065044","https://openalex.org/W2110335151","https://openalex.org/W2113551702","https://openalex.org/W2119498937","https://openalex.org/W2119904585","https://openalex.org/W2122029391","https://openalex.org/W2122245399","https://openalex.org/W2123707618","https://openalex.org/W2128716813","https://openalex.org/W2130479394","https://openalex.org/W2132023322","https://openalex.org/W2132926880","https://openalex.org/W2133347001","https://openalex.org/W2133585817","https://openalex.org/W2135230723","https://openalex.org/W2136101247","https://openalex.org/W2137991504","https://openalex.org/W2141292707","https://openalex.org/W2143320037","https://openalex.org/W2144368480","https://openalex.org/W2144954642","https://openalex.org/W2147850946","https://openalex.org/W2148643172","https://openalex.org/W2149531726","https://openalex.org/W2153947061","https://openalex.org/W2154539700","https://openalex.org/W2155469822","https://openalex.org/W2157362913","https://openalex.org/W2158217645","https://openalex.org/W2158714788","https://openalex.org/W2160545136","https://openalex.org/W2167133711","https://openalex.org/W2171187461","https://openalex.org/W2284827612","https://openalex.org/W2413508140"],"related_works":["https://openalex.org/W4229549692","https://openalex.org/W2765286129","https://openalex.org/W2033694563","https://openalex.org/W2014192257","https://openalex.org/W2994291374","https://openalex.org/W1859184435","https://openalex.org/W12279734","https://openalex.org/W2058766820","https://openalex.org/W4255542154","https://openalex.org/W4321748640"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}