{"id":"https://openalex.org/W2081801477","doi":"https://doi.org/10.1515/bams-2014-0013","title":"Opportunities and limitations in applying coevolution-derived contacts to protein structure prediction","display_name":"Opportunities and limitations in applying coevolution-derived contacts to protein structure prediction","publication_year":2014,"publication_date":"2014-11-27","ids":{"openalex":"https://openalex.org/W2081801477","doi":"https://doi.org/10.1515/bams-2014-0013","mag":"2081801477"},"language":"en","primary_location":{"id":"doi:10.1515/bams-2014-0013","is_oa":false,"landing_page_url":"https://doi.org/10.1515/bams-2014-0013","pdf_url":null,"source":{"id":"https://openalex.org/S2764861201","display_name":"Bio-Algorithms and Med-Systems","issn_l":"1895-9091","issn":["1895-9091","1896-530X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310313990","host_organization_name":"De Gruyter","host_organization_lineage":["https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bio-Algorithms and Med-Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017531384","display_name":"Stuart Tetchner","orcid":null},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stuart Tetchner","raw_affiliation_strings":["Department of Computer Science, University College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084827722","display_name":"Tomasz Ko\u015bci\u00f3\u0142ek","orcid":"https://orcid.org/0000-0002-9915-7387"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Tomasz Kosciolek","raw_affiliation_strings":["Department of Computer Science, University College London, London, UK"],"raw_orcid":"https://orcid.org/0000-0002-9915-7387","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068654082","display_name":"David T. Jones","orcid":"https://orcid.org/0000-0001-8626-3765"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"David T. Jones","raw_affiliation_strings":["Department of Computer Science, University College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5068654082"],"corresponding_institution_ids":["https://openalex.org/I45129253"],"apc_list":null,"apc_paid":null,"fwci":0.698,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.69784159,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"10","issue":"4","first_page":"243","last_page":"254"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994000196456909,"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":0.9994000196456909,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9948999881744385,"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":0.9941999912261963,"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/coevolution","display_name":"Coevolution","score":0.648381769657135},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5876808166503906},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5517133474349976},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.46799322962760925},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.4425153434276581},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.40718674659729004},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3678737282752991},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3391076326370239},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22438940405845642},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.10761448740959167},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09019795060157776},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06166696548461914}],"concepts":[{"id":"https://openalex.org/C33009525","wikidata":"https://www.wikidata.org/wiki/Q208841","display_name":"Coevolution","level":2,"score":0.648381769657135},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5876808166503906},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5517133474349976},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.46799322962760925},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.4425153434276581},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.40718674659729004},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3678737282752991},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3391076326370239},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22438940405845642},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.10761448740959167},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09019795060157776},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06166696548461914},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1515/bams-2014-0013","is_oa":false,"landing_page_url":"https://doi.org/10.1515/bams-2014-0013","pdf_url":null,"source":{"id":"https://openalex.org/S2764861201","display_name":"Bio-Algorithms and Med-Systems","issn_l":"1895-9091","issn":["1895-9091","1896-530X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310313990","host_organization_name":"De Gruyter","host_organization_lineage":["https://openalex.org/P4310313990"],"host_organization_lineage_names":["De Gruyter"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bio-Algorithms and Med-Systems","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4099999964237213}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":79,"referenced_works":["https://openalex.org/W1493324970","https://openalex.org/W1508885706","https://openalex.org/W1514077080","https://openalex.org/W1536428180","https://openalex.org/W1853158677","https://openalex.org/W1936662467","https://openalex.org/W1946569870","https://openalex.org/W1965839094","https://openalex.org/W1967600844","https://openalex.org/W1969836305","https://openalex.org/W1976666280","https://openalex.org/W1979762151","https://openalex.org/W1982420443","https://openalex.org/W1984765576","https://openalex.org/W1985115397","https://openalex.org/W1988695007","https://openalex.org/W1992613346","https://openalex.org/W1994983243","https://openalex.org/W1995017064","https://openalex.org/W2007230848","https://openalex.org/W2007506872","https://openalex.org/W2008545402","https://openalex.org/W2010577059","https://openalex.org/W2013425283","https://openalex.org/W2015470526","https://openalex.org/W2016984855","https://openalex.org/W2017421343","https://openalex.org/W2021769301","https://openalex.org/W2023346730","https://openalex.org/W2032647411","https://openalex.org/W2033806446","https://openalex.org/W2034557959","https://openalex.org/W2045777307","https://openalex.org/W2048154580","https://openalex.org/W2048310584","https://openalex.org/W2051210555","https://openalex.org/W2051545676","https://openalex.org/W2052935924","https://openalex.org/W2054291744","https://openalex.org/W2061042699","https://openalex.org/W2065921821","https://openalex.org/W2069319961","https://openalex.org/W2085036090","https://openalex.org/W2085211779","https://openalex.org/W2087455060","https://openalex.org/W2101220662","https://openalex.org/W2102864100","https://openalex.org/W2106119381","https://openalex.org/W2107517961","https://openalex.org/W2107867854","https://openalex.org/W2108559568","https://openalex.org/W2114340287","https://openalex.org/W2118265845","https://openalex.org/W2119843684","https://openalex.org/W2121114445","https://openalex.org/W2121444044","https://openalex.org/W2122011799","https://openalex.org/W2128819145","https://openalex.org/W2130479394","https://openalex.org/W2131848438","https://openalex.org/W2132555912","https://openalex.org/W2137566700","https://openalex.org/W2139271731","https://openalex.org/W2139447922","https://openalex.org/W2139754669","https://openalex.org/W2142796125","https://openalex.org/W2143210482","https://openalex.org/W2146849562","https://openalex.org/W2146891463","https://openalex.org/W2147526198","https://openalex.org/W2149729127","https://openalex.org/W2151831732","https://openalex.org/W2154369420","https://openalex.org/W2158343751","https://openalex.org/W2159409048","https://openalex.org/W2166701319","https://openalex.org/W2171641243","https://openalex.org/W2898667201","https://openalex.org/W2962971803"],"related_works":["https://openalex.org/W2946599741","https://openalex.org/W2593264178","https://openalex.org/W2043066834","https://openalex.org/W3171039768","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2058542300","https://openalex.org/W1564749278","https://openalex.org/W2294851134","https://openalex.org/W3215498386"],"abstract_inverted_index":{"Abstract":[0],"The":[1],"prospect":[2],"of":[3,51,54,65,78,90,96,113],"identifying":[4,36,84],"contacts":[5,38,56,79],"in":[6,80,99,110],"protein":[7,12],"structures":[8],"purely":[9],"from":[10,39],"aligned":[11],"sequences":[13],"has":[14,23],"lured":[15],"researchers":[16],"for":[17,35,70],"a":[18],"long":[19],"time,":[20],"but":[21],"progress":[22],"been":[24],"modest":[25],"until":[26],"recently.":[27],"Here,":[28],"we":[29,105],"reviewed":[30],"the":[31,52,63,75,85,88,94,107,111,118,126],"most":[32],"successful":[33],"methods":[34,44,67,98],"structural":[37],"sequence":[40,127],"and":[41,46,68,73,93,129],"how":[42],"these":[43,66,97],"differ":[45],"made":[47],"an":[48],"initial":[49],"assessment":[50],"overlap":[53],"predicted":[55],"by":[57,121],"alternative":[58,101],"approaches.":[59],"We":[60],"then":[61],"discussed":[62],"limitations":[64,119],"possibilities":[69],"future":[71,131],"development":[72],"highlighted":[74],"recent":[76],"applications":[77],"tertiary":[81],"structure":[82],"prediction,":[83,115],"residues":[86],"at":[87],"interfaces":[89],"protein-protein":[91],"interactions,":[92],"use":[95],"disentangling":[100],"conformational":[102],"states.":[103],"Finally,":[104],"identified":[106],"current":[108],"challenges":[109],"field":[112],"contact":[114],"concentrating":[116],"on":[117,125],"imposed":[120],"available":[122],"data,":[123],"dependencies":[124],"alignments,":[128],"possible":[130],"developments.":[132]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
