{"id":"https://openalex.org/W2214840940","doi":"https://doi.org/10.1109/bibm.2015.7359933","title":"Residue-residue contact prediction in the HIV-1 envelope glycoprotein complex","display_name":"Residue-residue contact prediction in the HIV-1 envelope glycoprotein complex","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2214840940","doi":"https://doi.org/10.1109/bibm.2015.7359933","mag":"2214840940"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2015.7359933","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359933","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-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/A5089740833","display_name":"Reda Rawi","orcid":"https://orcid.org/0000-0002-0445-2325"},"institutions":[{"id":"https://openalex.org/I4210144839","display_name":"Hamad bin Khalifa University","ror":"https://ror.org/03eyq4y97","country_code":"QA","type":"education","lineage":["https://openalex.org/I4210144839"]}],"countries":["QA"],"is_corresponding":false,"raw_author_name":"Reda Rawi","raw_affiliation_strings":["Computational Science and Engineering, Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Science and Engineering, Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar","institution_ids":["https://openalex.org/I4210144839"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067973729","display_name":"Khalid Kunji","orcid":"https://orcid.org/0000-0003-2946-512X"},"institutions":[{"id":"https://openalex.org/I4210144839","display_name":"Hamad bin Khalifa University","ror":"https://ror.org/03eyq4y97","country_code":"QA","type":"education","lineage":["https://openalex.org/I4210144839"]}],"countries":["QA"],"is_corresponding":false,"raw_author_name":"Khalid Kunji","raw_affiliation_strings":["Computational Science and Engineering, Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Science and Engineering, Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar","institution_ids":["https://openalex.org/I4210144839"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066466430","display_name":"Abdelali Haoudi","orcid":null},"institutions":[{"id":"https://openalex.org/I1288882113","display_name":"Boston Children's Hospital","ror":"https://ror.org/00dvg7y05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288882113"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I2802517405","display_name":"King Abdulaziz Medical City","ror":"https://ror.org/009djsq06","country_code":"SA","type":"healthcare","lineage":["https://openalex.org/I2802517405"]},{"id":"https://openalex.org/I4210095597","display_name":"King Abdullah International Medical Research Center","ror":"https://ror.org/009p8zv69","country_code":"SA","type":"facility","lineage":["https://openalex.org/I4210095597"]}],"countries":["SA","US"],"is_corresponding":false,"raw_author_name":"Abdelali Haoudi","raw_affiliation_strings":["Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA","King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I1288882113","https://openalex.org/I136199984"]},{"raw_affiliation_string":"King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh, Saudi Arabia","institution_ids":["https://openalex.org/I2802517405","https://openalex.org/I4210095597"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013350725","display_name":"Halima Bensmail","orcid":"https://orcid.org/0000-0001-6700-5752"},"institutions":[{"id":"https://openalex.org/I4210144839","display_name":"Hamad bin Khalifa University","ror":"https://ror.org/03eyq4y97","country_code":"QA","type":"education","lineage":["https://openalex.org/I4210144839"]}],"countries":["QA"],"is_corresponding":false,"raw_author_name":"Halima Bensmail","raw_affiliation_strings":["Computational Science and Engineering, Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Science and Engineering, Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar","institution_ids":["https://openalex.org/I4210144839"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08374978,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"90","issue":null,"first_page":"1709","last_page":"1711"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10112","display_name":"HIV Research and Treatment","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980999827384949,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gp41","display_name":"Gp41","score":0.8497695922851562},{"id":"https://openalex.org/keywords/glycoprotein","display_name":"Glycoprotein","score":0.6957144737243652},{"id":"https://openalex.org/keywords/viral-entry","display_name":"Viral entry","score":0.5543510317802429},{"id":"https://openalex.org/keywords/v3-loop","display_name":"V3 loop","score":0.5372071266174316},{"id":"https://openalex.org/keywords/viral-envelope","display_name":"Viral envelope","score":0.5264186263084412},{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.47495174407958984},{"id":"https://openalex.org/keywords/plasma-protein-binding","display_name":"Plasma protein binding","score":0.4706869423389435},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.46372315287590027},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45724865794181824},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.45191556215286255},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4352877140045166},{"id":"https://openalex.org/keywords/chemokine-receptor","display_name":"Chemokine receptor","score":0.4251558184623718},{"id":"https://openalex.org/keywords/lipid-bilayer-fusion","display_name":"Lipid bilayer fusion","score":0.4168757200241089},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.39137300848960876},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3405989110469818},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.3333069682121277},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.3047793507575989},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.27776065468788147},{"id":"https://openalex.org/keywords/viral-replication","display_name":"Viral replication","score":0.23788446187973022},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.23077112436294556},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.22357866168022156},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.22176271677017212},{"id":"https://openalex.org/keywords/chemokine","display_name":"Chemokine","score":0.21807849407196045},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19286823272705078},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.10802841186523438},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08785954117774963}],"concepts":[{"id":"https://openalex.org/C2776258796","wikidata":"https://www.wikidata.org/wiki/Q5590520","display_name":"Gp41","level":4,"score":0.8497695922851562},{"id":"https://openalex.org/C108625454","wikidata":"https://www.wikidata.org/wiki/Q187126","display_name":"Glycoprotein","level":2,"score":0.6957144737243652},{"id":"https://openalex.org/C58475186","wikidata":"https://www.wikidata.org/wiki/Q4118894","display_name":"Viral entry","level":4,"score":0.5543510317802429},{"id":"https://openalex.org/C2779921545","wikidata":"https://www.wikidata.org/wiki/Q12085358","display_name":"V3 loop","level":4,"score":0.5372071266174316},{"id":"https://openalex.org/C97380033","wikidata":"https://www.wikidata.org/wiki/Q994215","display_name":"Viral envelope","level":3,"score":0.5264186263084412},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.47495174407958984},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.4706869423389435},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.46372315287590027},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45724865794181824},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.45191556215286255},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4352877140045166},{"id":"https://openalex.org/C12823836","wikidata":"https://www.wikidata.org/wiki/Q24720618","display_name":"Chemokine receptor","level":4,"score":0.4251558184623718},{"id":"https://openalex.org/C103038307","wikidata":"https://www.wikidata.org/wiki/Q6556360","display_name":"Lipid bilayer fusion","level":3,"score":0.4168757200241089},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.39137300848960876},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3405989110469818},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.3333069682121277},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3047793507575989},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.27776065468788147},{"id":"https://openalex.org/C140704245","wikidata":"https://www.wikidata.org/wiki/Q3933202","display_name":"Viral replication","level":3,"score":0.23788446187973022},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.23077112436294556},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.22357866168022156},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.22176271677017212},{"id":"https://openalex.org/C13373296","wikidata":"https://www.wikidata.org/wiki/Q421866","display_name":"Chemokine","level":3,"score":0.21807849407196045},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19286823272705078},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.10802841186523438},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08785954117774963}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2015.7359933","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2015.7359933","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6800000071525574,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1979646413","https://openalex.org/W1995924392","https://openalex.org/W2004622809","https://openalex.org/W2008545402","https://openalex.org/W2020736655","https://openalex.org/W2023346730","https://openalex.org/W2065921821","https://openalex.org/W2074179519","https://openalex.org/W2091765515","https://openalex.org/W2092006899","https://openalex.org/W2099308199","https://openalex.org/W2119843684","https://openalex.org/W2130479394","https://openalex.org/W2146891463","https://openalex.org/W2154643316","https://openalex.org/W2166701319","https://openalex.org/W2171641243"],"related_works":["https://openalex.org/W2316191615","https://openalex.org/W2072253684","https://openalex.org/W2094214456","https://openalex.org/W2143312620","https://openalex.org/W3157219655","https://openalex.org/W2557158036","https://openalex.org/W2067569784","https://openalex.org/W2168425791","https://openalex.org/W2503324635","https://openalex.org/W4321365856"],"abstract_inverted_index":{"HIV-1":[0,14,67,132],"Env":[1,68,133],"glycoprotein":[2],"complex":[3,20,77],"is":[4,109],"the":[5,28,30,37,43,51,60,107,127,153,161],"key":[6],"protein":[7,134,193],"that":[8,62],"mediates":[9],"binding":[10],"and":[11,34,49,55,85,90,99,103,129,158,176,197,201],"entry":[12,21,108,203],"of":[13,32,53,66,86,96,131,151,185],"into":[15],"human":[16],"host":[17,56],"cells.":[18],"The":[19],"process":[22],"involves":[23],"three":[24],"main":[25],"steps.":[26],"First,":[27],"attachment,":[29],"interaction":[31,122],"gp120":[33,41,102],"CD4.":[35],"Second,":[36],"coreceptor":[38],"binding,":[39,172],"where":[40],"binds":[42],"chemokine":[44],"receptor":[45,171],"CCR5":[46],"or":[47,82,165],"CXCR4,":[48],"finally,":[50],"fusion":[52],"viral":[54],"cell":[57],"membranes.":[58],"Despite":[59],"fact":[61],"several":[63],"coordinate":[64,163,194],"structures":[65],"in":[69,76,88,160,187,191,198],"unliganded":[70],"state":[71],"exist":[72],"(as":[73],"well":[74],"as":[75,170],"with":[78],"CD4,":[79],"CD4":[80],"mimics,":[81],"various":[83],"antibodies,":[84],"gp41":[87,104],"intermediate":[89],"post-fusion":[91],"state),":[92],"a":[93,118,182],"comprehensive":[94],"understanding":[95],"structural":[97],"arrangements":[98],"communication":[100],"within":[101,149],"domains":[105],"during":[106],"far":[110],"from":[111],"complete.":[112],"In":[113],"this":[114],"study,":[115],"we":[116],"applied":[117],"direct":[119],"amino":[120],"acid":[121],"detecting":[123],"method":[124],"to":[125],"analyse":[126],"function":[128],"structure":[130,195],"sequences":[135],"representing":[136],"all":[137],"group":[138],"M":[139],"subtypes.":[140],"We":[141],"identified":[142],"more":[143],"than":[144],"400":[145],"coevolving":[146],"residue":[147],"pairs":[148],"Env,":[150],"which":[152],"majority":[154],"are":[155],"real":[156],"contacts":[157],"proximal":[159],"available":[162],"structures,":[164],"have":[166],"functional":[167],"implications":[168],"such":[169],"variable":[173],"loop,":[174],"gp120-gp41,":[175],"interdomain":[177],"interactions.":[178],"This":[179],"work":[180],"provides":[181],"new":[183,200],"dimension":[184],"information":[186],"HIV":[188],"research,":[189],"important":[190],"assisting":[192],"prediction":[196],"designing":[199],"effective":[202],"inhibitors.":[204]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}