{"id":"https://openalex.org/W2258637354","doi":"https://doi.org/10.1109/tcbb.2016.2520923","title":"Extracting Coevolutionary Features from Protein Sequences for Predicting Protein-Protein Interactions","display_name":"Extracting Coevolutionary Features from Protein Sequences for Predicting Protein-Protein Interactions","publication_year":2016,"publication_date":"2016-01-22","ids":{"openalex":"https://openalex.org/W2258637354","doi":"https://doi.org/10.1109/tcbb.2016.2520923","mag":"2258637354","pmid":"https://pubmed.ncbi.nlm.nih.gov/26812730"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2016.2520923","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2016.2520923","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5008221100","display_name":"Lun Hu","orcid":"https://orcid.org/0000-0002-1591-8549"},"institutions":[{"id":"https://openalex.org/I14243506","display_name":"Hong Kong Polytechnic University","ror":"https://ror.org/0030zas98","country_code":"HK","type":"education","lineage":["https://openalex.org/I14243506"]},{"id":"https://openalex.org/I196699116","display_name":"Wuhan University of Technology","ror":"https://ror.org/03fe7t173","country_code":"CN","type":"education","lineage":["https://openalex.org/I196699116"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Lun Hu","raw_affiliation_strings":["Department of Computing, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China","School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China","institution_ids":["https://openalex.org/I14243506"]},{"raw_affiliation_string":"School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I196699116"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107049960","display_name":"Keith C. C. Chan","orcid":"https://orcid.org/0000-0001-7962-6564"},"institutions":[{"id":"https://openalex.org/I14243506","display_name":"Hong Kong Polytechnic University","ror":"https://ror.org/0030zas98","country_code":"HK","type":"education","lineage":["https://openalex.org/I14243506"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Keith C.C. Chan","raw_affiliation_strings":["Department of Computing, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China","institution_ids":["https://openalex.org/I14243506"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.1222,"has_fulltext":false,"cited_by_count":45,"citation_normalized_percentile":{"value":0.77825741,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"14","issue":"1","first_page":"155","last_page":"166"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9988999962806702,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9983000159263611,"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/feature","display_name":"Feature (linguistics)","score":0.6159815788269043},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5975766777992249},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.5641151070594788},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5395672917366028},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5236330032348633},{"id":"https://openalex.org/keywords/feature-vector","display_name":"Feature vector","score":0.5048009157180786},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.47755417227745056},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.47707903385162354},{"id":"https://openalex.org/keywords/feature-extraction","display_name":"Feature extraction","score":0.46806612610816956},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4486534297466278},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4115484654903412},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31406041979789734},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18422898650169373},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.16342389583587646},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12839552760124207}],"concepts":[{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.6159815788269043},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5975766777992249},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.5641151070594788},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5395672917366028},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5236330032348633},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.5048009157180786},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.47755417227745056},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47707903385162354},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.46806612610816956},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4486534297466278},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4115484654903412},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31406041979789734},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18422898650169373},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.16342389583587646},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12839552760124207},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"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":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"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":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2016.2520923","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2016.2520923","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26812730","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26812730","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6546667233","display_name":null,"funder_award_id":"2016IVA051","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1533936090","https://openalex.org/W1575542444","https://openalex.org/W1583876435","https://openalex.org/W1596717185","https://openalex.org/W1817561967","https://openalex.org/W1971227936","https://openalex.org/W1974515660","https://openalex.org/W1982267716","https://openalex.org/W1984765576","https://openalex.org/W1990212480","https://openalex.org/W1992271736","https://openalex.org/W2015407064","https://openalex.org/W2029286575","https://openalex.org/W2037036397","https://openalex.org/W2045131140","https://openalex.org/W2057885377","https://openalex.org/W2068446924","https://openalex.org/W2071502814","https://openalex.org/W2074097214","https://openalex.org/W2081931663","https://openalex.org/W2085075228","https://openalex.org/W2087322782","https://openalex.org/W2096525273","https://openalex.org/W2099862356","https://openalex.org/W2105924489","https://openalex.org/W2107340752","https://openalex.org/W2107424557","https://openalex.org/W2120770540","https://openalex.org/W2122863289","https://openalex.org/W2125107234","https://openalex.org/W2132582966","https://openalex.org/W2133990480","https://openalex.org/W2134197776","https://openalex.org/W2145080853","https://openalex.org/W2145427519","https://openalex.org/W2146312020","https://openalex.org/W2146764011","https://openalex.org/W2149310258","https://openalex.org/W2150452800","https://openalex.org/W2152568394","https://openalex.org/W2153635508","https://openalex.org/W2155004936","https://openalex.org/W2161701113","https://openalex.org/W2162038040","https://openalex.org/W2164289561","https://openalex.org/W2167869241","https://openalex.org/W2408289238","https://openalex.org/W2911964244","https://openalex.org/W3139910489","https://openalex.org/W4245543257","https://openalex.org/W4252706339"],"related_works":["https://openalex.org/W2366107444","https://openalex.org/W4388145910","https://openalex.org/W2381570729","https://openalex.org/W1976205134","https://openalex.org/W4248336175","https://openalex.org/W2183771695","https://openalex.org/W2003790670","https://openalex.org/W100270783","https://openalex.org/W1976952616","https://openalex.org/W3107297455"],"abstract_inverted_index":{"Knowing":[0],"the":[1,14,40,46,142,150,176,180,197,218,226,235,268],"ways":[2],"proteins":[3,98,118,248],"interact":[4,119],"with":[5,120],"each":[6,82,121],"other":[7,122,177],"are":[8,43,99,144],"crucial":[9],"to":[10,32,45,58,72,102,153,158,185,217],"our":[11],"understanding":[12],"of":[13,17,68,94,97,106,113,166,175,230,237,247,270],"functional":[15],"mechanisms":[16],"proteins.":[18,110,252],"It":[19],"is":[20,123,259],"for":[21,81,245],"this":[22],"reason":[23],"that":[24,80,145,257],"different":[25],"approaches":[26,42,65],"have":[27],"been":[28],"developed":[29],"in":[30,179,192,234],"attempts":[31],"predict":[33],"protein-protein":[34],"interactions":[35],"(PPIs)":[36],"computationally.":[37],"Among":[38],"them,":[39],"sequence-based":[41,64],"preferred":[44],"others":[47],"as":[48,126],"they":[49],"do":[50,163],"not":[51,116],"require":[52],"any":[53],"information":[54],"about":[55],"protein":[56,77,83,151,172,178,194],"properties":[57],"perform":[59],"their":[60],"tasks.":[61],"Instead,":[62],"most":[63],"make":[66],"use":[67],"feature":[69,89,92,198,206,240,262],"extraction":[70,199,207,263],"methods":[71],"extract":[73],"features":[74,143,169,188,212,233],"directly":[75],"from":[76,149,170,189],"sequences":[78,152,173,191,236],"so":[79],"sequence,":[84],"we":[85,183],"can":[86,134,146,242,266],"construct":[87],"a":[88,127,193,203,260],"vector.":[90],"The":[91,111,253],"vectors":[93,241],"every":[95],"pair":[96,195],"then":[100,124],"concatenated":[101],"form":[103],"two":[104,117,238],"classes":[105],"interacting":[107,155],"and":[108,228,265],"non-interacting":[109,157],"prediction":[112],"whether":[114],"or":[115,156],"formulated":[125],"classification":[128],"problem.":[129],"How":[130],"accurate":[131],"PPI":[132,271],"predictions":[133],"be":[135,147,159,243],"made":[136],"therefore":[137],"depends":[138],"on":[139,225],"how":[140],"good":[141],"extracted":[148,213],"allow":[154],"best":[160],"distinguished.":[161],"To":[162],"so,":[164],"instead":[165],"extracting":[167],"such":[168],"individual":[171,251],"independently":[174],"same":[181],"pair,":[182],"propose":[184],"jointly":[186],"consider":[187],"both":[190],"during":[196],"process":[200],"through":[201],"using":[202],"novel":[204],"coevolutionary":[205,232],"approach":[208,264],"called":[209],"CoFex.":[210],"Coevolutionary":[211],"by":[214],"CoFex":[215,258],"refer":[216],"covariations":[219],"found":[220],"at":[221],"coevolving":[222],"positions.":[223],"Based":[224],"presence":[227],"absence":[229],"these":[231],"proteins,":[239],"composed":[244],"pairs":[246],"rather":[249],"than":[250],"experiment":[254],"results":[255],"show":[256],"promising":[261],"improve":[267],"performance":[269],"prediction.":[272]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
