{"id":"https://openalex.org/W2108130002","doi":"https://doi.org/10.1142/s021972001441008x","title":"Co-evolution analysis to predict protein\u2013protein interactions within influenza virus envelope","display_name":"Co-evolution analysis to predict protein\u2013protein interactions within influenza virus envelope","publication_year":2014,"publication_date":"2014-03-06","ids":{"openalex":"https://openalex.org/W2108130002","doi":"https://doi.org/10.1142/s021972001441008x","mag":"2108130002","pmid":"https://pubmed.ncbi.nlm.nih.gov/24712535"},"language":"en","primary_location":{"id":"doi:10.1142/s021972001441008x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972001441008x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5042758370","display_name":"R. R. Mintaev","orcid":"https://orcid.org/0000-0001-5398-3627"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Ramil R. Mintaev","raw_affiliation_strings":["Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1-40, Moscow 119991, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1-40, Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056758947","display_name":"Andrei V. Alexeevski","orcid":"https://orcid.org/0000-0001-7939-9939"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Andrei V. Alexeevski","raw_affiliation_strings":["Department of Bioengineering and Bioinformatics & Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1-73 & 1-40, Moscow 119991, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering and Bioinformatics & Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1-73 & 1-40, Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021986271","display_name":"Larisa V. Kordyukova","orcid":"https://orcid.org/0000-0002-6089-1103"},"institutions":[{"id":"https://openalex.org/I19880235","display_name":"Lomonosov Moscow State University","ror":"https://ror.org/010pmpe69","country_code":"RU","type":"education","lineage":["https://openalex.org/I19880235"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"Larisa V. Kordyukova","raw_affiliation_strings":["Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1-40, Moscow 119991, Russia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Belozersky Institute of Physico-Chemical Biology, Moscow State University, Leninskie Gory 1-40, Moscow 119991, Russia","institution_ids":["https://openalex.org/I19880235"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I19880235"],"apc_list":null,"apc_paid":null,"fwci":0.4313,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.67593225,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"12","issue":"02","first_page":"1441008","last_page":"1441008"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":1.0,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9973999857902527,"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":0.9955999851226807,"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/viral-matrix-protein","display_name":"Viral matrix protein","score":0.6447010040283203},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.6302714347839355},{"id":"https://openalex.org/keywords/hemagglutinin","display_name":"Hemagglutinin (influenza)","score":0.6103729605674744},{"id":"https://openalex.org/keywords/neuraminidase","display_name":"Neuraminidase","score":0.5815764665603638},{"id":"https://openalex.org/keywords/influenza-a-virus","display_name":"Influenza A virus","score":0.5277569890022278},{"id":"https://openalex.org/keywords/protein-methods","display_name":"Protein methods","score":0.48448535799980164},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.48195502161979675},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4707377851009369},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.3977346420288086},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.3927821218967438},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3571665287017822},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.35337743163108826},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32914993166923523},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18727731704711914}],"concepts":[{"id":"https://openalex.org/C68434959","wikidata":"https://www.wikidata.org/wiki/Q1908996","display_name":"Viral matrix protein","level":3,"score":0.6447010040283203},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.6302714347839355},{"id":"https://openalex.org/C2778692840","wikidata":"https://www.wikidata.org/wiki/Q9136673","display_name":"Hemagglutinin (influenza)","level":3,"score":0.6103729605674744},{"id":"https://openalex.org/C134164806","wikidata":"https://www.wikidata.org/wiki/Q409485","display_name":"Neuraminidase","level":3,"score":0.5815764665603638},{"id":"https://openalex.org/C2777546802","wikidata":"https://www.wikidata.org/wiki/Q834390","display_name":"Influenza A virus","level":3,"score":0.5277569890022278},{"id":"https://openalex.org/C111364199","wikidata":"https://www.wikidata.org/wiki/Q2915896","display_name":"Protein methods","level":4,"score":0.48448535799980164},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.48195502161979675},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4707377851009369},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3977346420288086},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.3927821218967438},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3571665287017822},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.35337743163108826},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32914993166923523},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18727731704711914}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D000595","descriptor_name":"Amino Acid Sequence","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":"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":"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":"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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014759","descriptor_name":"Viral Envelope Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014759","descriptor_name":"Viral Envelope Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014759","descriptor_name":"Viral Envelope Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014759","descriptor_name":"Viral Envelope Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014759","descriptor_name":"Viral Envelope Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014759","descriptor_name":"Viral Envelope Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":3,"locations":[{"id":"doi:10.1142/s021972001441008x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972001441008x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:24712535","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24712535","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":"Journal of bioinformatics and computational biology","raw_type":null},{"id":"mag:2276964253","is_oa":false,"landing_page_url":"https://istina.msu.ru/publications/article/9003047/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.6200000047683716,"display_name":"Life in Land"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1919873525","https://openalex.org/W1926196563","https://openalex.org/W1970432249","https://openalex.org/W1982583124","https://openalex.org/W1985064062","https://openalex.org/W1988044361","https://openalex.org/W1990151313","https://openalex.org/W1993829010","https://openalex.org/W1999220414","https://openalex.org/W2002815902","https://openalex.org/W2004313038","https://openalex.org/W2008545402","https://openalex.org/W2017562106","https://openalex.org/W2022396428","https://openalex.org/W2030104209","https://openalex.org/W2031121531","https://openalex.org/W2034244874","https://openalex.org/W2037115572","https://openalex.org/W2044339598","https://openalex.org/W2051816135","https://openalex.org/W2061042699","https://openalex.org/W2073521270","https://openalex.org/W2083130194","https://openalex.org/W2102335249","https://openalex.org/W2109285534","https://openalex.org/W2111152104","https://openalex.org/W2119362018","https://openalex.org/W2129534059","https://openalex.org/W2135553224","https://openalex.org/W2140597030","https://openalex.org/W2142061382","https://openalex.org/W2143001591","https://openalex.org/W2147897601","https://openalex.org/W2148284376","https://openalex.org/W2154643316","https://openalex.org/W2157267331","https://openalex.org/W2160999362","https://openalex.org/W2267354562"],"related_works":["https://openalex.org/W4248770357","https://openalex.org/W2077900088","https://openalex.org/W2366312862","https://openalex.org/W2096565446","https://openalex.org/W4312067611","https://openalex.org/W2056993909","https://openalex.org/W2417585499","https://openalex.org/W1970078779","https://openalex.org/W2347657080","https://openalex.org/W2108130002"],"abstract_inverted_index":{"Interactions":[0],"between":[1],"integral":[2],"membrane":[3],"proteins":[4,44],"hemagglutinin":[5],"(HA),":[6],"neuraminidase":[7],"(NA),":[8],"M2":[9,93],"and":[10,49,92,124,131,146],"membrane-associated":[11],"matrix":[12],"protein":[13,109,133,196],"M1":[14,102],"of":[15,26,41,75,101,115,154,161,173,194],"influenza":[16],"A":[17],"virus":[18],"are":[19,45],"thought":[20],"to":[21,151,178,183],"be":[22],"crucial":[23],"for":[24,72,128,143,164],"assembly":[25],"functionally":[27],"competent":[28],"virions.":[29],"We":[30],"hypothesized":[31],"that":[32],"the":[33,39,58,65,89,104,108,155,189,199],"amino":[34,76,167],"acid":[35,77,168],"residues":[36],"located":[37],"at":[38],"interface":[40],"two":[42,165],"different":[43],"under":[46],"physical":[47],"constraints":[48],"thus":[50],"probably":[51],"co-evolve.":[52],"To":[53],"predict":[54],"co-evolving":[55],"residue":[56],"pairs,":[57,134],"EvFold":[59],"(":[60,83],"http://evfold.org":[61],")":[62],"program":[63],"searching":[64],"(nontransitive)":[66],"Direct":[67],"Information":[68],"scores":[69],"was":[70,176,202],"applied":[71],"large":[73],"samplings":[74],"sequences":[78],"from":[79],"Influenza":[80],"Research":[81],"Database":[82],"http://www.fludb.org/":[84],").":[85],"Having":[86],"focused":[87],"on":[88,188],"HA,":[90],"NA,":[91],"cytoplasmic":[94,157],"tails":[95],"as":[96,98],"well":[97],"C-terminal":[99],"domain":[100],"(being":[103],"less":[105],"conserved":[106],"among":[107],"domains)":[110],"we":[111],"captured":[112],"six":[113],"pairs":[114,127,148,172],"correlated":[116,174],"positions.":[117],"Among":[118],"them,":[119],"there":[120],"were":[121,141],"one,":[122],"two,":[123],"three":[125],"position":[126],"HA-M2,":[129],"HA-M1,":[130],"M2-M1":[132],"respectively.":[135],"As":[136],"expected,":[137],"no":[138],"co-varying":[139],"positions":[140,175],"found":[142],"NA-HA,":[144],"NA-M1,":[145],"NA-M2":[147],"obviously":[149],"due":[150],"high":[152,182],"conservation":[153],"NA":[156],"tail.":[158],"The":[159],"sum":[160],"frequencies":[162],"calculated":[163],"major":[166],"patterns":[169],"observed":[170],"in":[171],"up":[177],"0.99":[179],"meaning":[180],"their":[181],"extreme":[184],"evolutionary":[185],"sustainability.":[186],"Based":[187],"predictions":[190],"a":[191],"hypothetical":[192],"model":[193],"pair-wise":[195],"interactions":[197],"within":[198],"viral":[200],"envelope":[201],"proposed.":[203]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}