{"id":"https://openalex.org/W2115185759","doi":"https://doi.org/10.1093/bib/bbm052","title":"Correlated substitution analysis and the prediction of amino acid structural contacts","display_name":"Correlated substitution analysis and the prediction of amino acid structural contacts","publication_year":2007,"publication_date":"2007-10-23","ids":{"openalex":"https://openalex.org/W2115185759","doi":"https://doi.org/10.1093/bib/bbm052","mag":"2115185759","pmid":"https://pubmed.ncbi.nlm.nih.gov/18000015"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbm052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbm052","pdf_url":"https://academic.oup.com/bib/article-pdf/9/1/46/824276/bbm052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/9/1/46/824276/bbm052.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032504955","display_name":"David S. Horner","orcid":"https://orcid.org/0000-0002-6739-2657"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"D. S. Horner","raw_affiliation_strings":["Department of Biomolecular Sciences and Biotechnology, University of Milan, via Celoria 26, 20133 Milano, Italy. David.horner@unimi.it","Department of Biomolecular Sciences and Biotechnology, University of Milan, Via Celoria 26, 20133, Milano, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Sciences and Biotechnology, University of Milan, via Celoria 26, 20133 Milano, Italy. David.horner@unimi.it","institution_ids":["https://openalex.org/I189158943"]},{"raw_affiliation_string":"Department of Biomolecular Sciences and Biotechnology, University of Milan, Via Celoria 26, 20133, Milano, Italy","institution_ids":["https://openalex.org/I189158943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016959285","display_name":"Walter Pirovano","orcid":"https://orcid.org/0000-0002-2717-4735"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"W. Pirovano","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5005312066","display_name":"Graziano Pesole","orcid":"https://orcid.org/0000-0003-3663-0859"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"G. Pesole","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032504955"],"corresponding_institution_ids":["https://openalex.org/I189158943"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.4091,"has_fulltext":false,"cited_by_count":93,"citation_normalized_percentile":{"value":0.88878082,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"9","issue":"1","first_page":"46","last_page":"56"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9995999932289124,"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":0.998199999332428,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6784546971321106},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.6679197549819946},{"id":"https://openalex.org/keywords/amino-acid-substitution","display_name":"Amino acid substitution","score":0.6599271297454834},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5583631992340088},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.5248080492019653},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.45798081159591675},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4439627230167389},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.43480414152145386},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4178471565246582},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4107588231563568},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39621442556381226},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3751427233219147},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3605915307998657},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.34975242614746094},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3361048400402069},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3004588484764099},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.15134072303771973},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11687394976615906},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10803714394569397}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6784546971321106},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.6679197549819946},{"id":"https://openalex.org/C2993683473","wikidata":"https://www.wikidata.org/wiki/Q30693176","display_name":"Amino acid substitution","level":4,"score":0.6599271297454834},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5583631992340088},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.5248080492019653},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.45798081159591675},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4439627230167389},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.43480414152145386},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4178471565246582},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4107588231563568},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39621442556381226},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3751427233219147},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3605915307998657},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.34975242614746094},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3361048400402069},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3004588484764099},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.15134072303771973},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11687394976615906},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10803714394569397},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"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":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"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":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":null,"qualifier_name":null,"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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbm052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbm052","pdf_url":"https://academic.oup.com/bib/article-pdf/9/1/46/824276/bbm052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18000015","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18000015","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:research.vu.nl:openaire/7c5be9c8-12c8-403c-94ff-6803d6f3d3ef","is_oa":true,"landing_page_url":"https://research.vu.nl/en/publications/7c5be9c8-12c8-403c-94ff-6803d6f3d3ef","pdf_url":null,"source":{"id":"https://openalex.org/S4306401107","display_name":"VU Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I865915315","host_organization_name":"Vrije Universiteit Amsterdam","host_organization_lineage":["https://openalex.org/I865915315"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Horner, D S, Pirovano, W & Pesole, G 2008, 'Correlated substitution analysis and the prediction of amino acid structural contacts', Briefings in bioinformatics, vol. 9, no. 1, pp. 46-56. https://doi.org/10.1093/bib/bbm052","raw_type":"article"},{"id":"pmh:oai:ricerca.uniba.it:11586/23731","is_oa":false,"landing_page_url":"http://hdl.handle.net/11586/23731","pdf_url":null,"source":{"id":"https://openalex.org/S4377196296","display_name":"CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I5561750","host_organization_name":"University of Bari Aldo Moro","host_organization_lineage":["https://openalex.org/I5561750"],"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":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbm052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbm052","pdf_url":"https://academic.oup.com/bib/article-pdf/9/1/46/824276/bbm052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2115185759.pdf","grobid_xml":"https://content.openalex.org/works/W2115185759.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W1593454066","https://openalex.org/W1978014862","https://openalex.org/W1979389134","https://openalex.org/W1994528559","https://openalex.org/W2009123297","https://openalex.org/W2017519756","https://openalex.org/W2021769301","https://openalex.org/W2025980842","https://openalex.org/W2027736929","https://openalex.org/W2029423438","https://openalex.org/W2031368570","https://openalex.org/W2033354942","https://openalex.org/W2034177352","https://openalex.org/W2034557959","https://openalex.org/W2046709696","https://openalex.org/W2052337946","https://openalex.org/W2085075228","https://openalex.org/W2086240831","https://openalex.org/W2087300028","https://openalex.org/W2092006899","https://openalex.org/W2094559779","https://openalex.org/W2096279929","https://openalex.org/W2097980499","https://openalex.org/W2099715859","https://openalex.org/W2099846003","https://openalex.org/W2100063856","https://openalex.org/W2103546861","https://openalex.org/W2104975318","https://openalex.org/W2108067237","https://openalex.org/W2110411038","https://openalex.org/W2110612888","https://openalex.org/W2113178668","https://openalex.org/W2116406204","https://openalex.org/W2116503869","https://openalex.org/W2117647295","https://openalex.org/W2119632499","https://openalex.org/W2120549641","https://openalex.org/W2121960367","https://openalex.org/W2126675814","https://openalex.org/W2126932544","https://openalex.org/W2129421547","https://openalex.org/W2131848438","https://openalex.org/W2135500937","https://openalex.org/W2137991504","https://openalex.org/W2141702919","https://openalex.org/W2141885858","https://openalex.org/W2142319534","https://openalex.org/W2143210482","https://openalex.org/W2147660889","https://openalex.org/W2151911385","https://openalex.org/W2152529266","https://openalex.org/W2154072371","https://openalex.org/W2154643316","https://openalex.org/W2158381555","https://openalex.org/W2158539318","https://openalex.org/W2159409048","https://openalex.org/W2163941254","https://openalex.org/W2166298363","https://openalex.org/W2171641243"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W1741740882","https://openalex.org/W2414840205","https://openalex.org/W2035942032"],"abstract_inverted_index":{"It":[0],"has":[1],"long":[2],"been":[3,44],"suspected":[4],"that":[5,19,160],"analysis":[6],"of":[7,17,56,58,75,83,92,100,110,135,150,171,186,195],"correlated":[8,68,163,196],"amino":[9,49,197],"acid":[10,198],"substitutions":[11,164],"should":[12,165],"uncover":[13],"pairs":[14,57,74],"or":[15],"clusters":[16],"sites":[18,59,136],"are":[20,69,138,144],"spatially":[21,76,140],"proximal":[22,77],"in":[23,73,90,95,146,179,204,211],"mature":[24],"protein":[25,101],"structures.":[26],"Accordingly,":[27],"methods":[28,66,191],"based":[29],"on":[30],"different":[31],"mathematical":[32],"principles":[33],"such":[34,88],"as":[35,67],"information":[36,161,172],"theory,":[37],"correlation":[38,124,134],"coefficients":[39],"and":[40,122,207],"maximum":[41],"likelihood":[42],"have":[43,158],"developed":[45],"to":[46,126,182],"identify":[47],"co-evolving":[48],"acids":[50],"from":[51,123,162],"multiple":[52],"sequence":[53],"alignments.":[54],"Sets":[55],"whose":[60],"behaviour":[61],"is":[62],"identified":[63],"by":[64,116],"these":[65],"often":[70],"significantly":[71],"enriched":[72],"residues.":[78],"However,":[79],"relatively":[80],"high":[81],"levels":[82],"false-positive":[84,187],"predictions":[85],"typically":[86],"render":[87],"methods,":[89],"isolation,":[91],"little":[93],"use":[94],"the":[96,108,151,184,193,212],"ab":[97],"initio":[98],"prediction":[99,206],"structure.":[102],"Misleading":[103],"signal":[104],"(or":[105],"problems":[106],"with":[107,168],"estimation":[109],"significance":[111],"levels)":[112],"can":[113],"be":[114,166],"caused":[115],"phylogenetic":[117],"correlations":[118],"between":[119],"homologous":[120],"sequences":[121],"due":[125],"factors":[127],"other":[128,169],"than":[129],"spatial":[130],"proximity":[131],"(for":[132],"example,":[133],"which":[137,143],"not":[139],"close":[141],"but":[142],"involved":[145],"common":[147],"functional":[148],"properties":[149],"protein).":[152],"In":[153],"recent":[154],"years,":[155],"several":[156],"workers":[157],"suggested":[159],"combined":[167],"sources":[170],"(secondary":[173],"structure,":[174],"solvent":[175],"accessibility,":[176],"evolutionary":[177],"rates)":[178],"an":[180],"attempt":[181],"reduce":[183],"proportion":[185],"predictions.":[188],"We":[189],"review":[190],"for":[192],"detection":[194],"substitutions,":[199],"compare":[200],"their":[201],"relative":[202],"performance":[203],"contact":[205],"predict":[208],"future":[209],"directions":[210],"field.":[213]},"counts_by_year":[{"year":2021,"cited_by_count":31},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":7}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-10T00:00:00"}
