{"id":"https://openalex.org/W2771166878","doi":"https://doi.org/10.1109/bibm.2017.8217632","title":"HIV1-human protein-protein interaction prediction based on interface architecture similarity","display_name":"HIV1-human protein-protein interaction prediction based on interface architecture similarity","publication_year":2017,"publication_date":"2017-11-01","ids":{"openalex":"https://openalex.org/W2771166878","doi":"https://doi.org/10.1109/bibm.2017.8217632","mag":"2771166878"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2017.8217632","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8217632","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 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/A5101571739","display_name":"Chunyu Zhao","orcid":"https://orcid.org/0000-0001-9589-2416"},"institutions":[{"id":"https://openalex.org/I1335321130","display_name":"Children's Hospital of Philadelphia","ror":"https://ror.org/01z7r7q48","country_code":"US","type":"funder","lineage":["https://openalex.org/I1335321130"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chunyu Zhao","raw_affiliation_strings":["PennCHOP Microbiome Program, Children's Hospital of Philadelphia, Philadelphia, US"],"affiliations":[{"raw_affiliation_string":"PennCHOP Microbiome Program, Children's Hospital of Philadelphia, Philadelphia, US","institution_ids":["https://openalex.org/I1335321130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054049776","display_name":"Yizhou Zang","orcid":null},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yizhou Zang","raw_affiliation_strings":["College of Computing and Informatics, Drexel University, Philadelphia, US"],"affiliations":[{"raw_affiliation_string":"College of Computing and Informatics, Drexel University, Philadelphia, US","institution_ids":["https://openalex.org/I72816309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082147952","display_name":"Wei Quan","orcid":"https://orcid.org/0000-0002-0934-8324"},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Quan","raw_affiliation_strings":["College of Computing and Informatics, Drexel University, Philadelphia, US"],"affiliations":[{"raw_affiliation_string":"College of Computing and Informatics, Drexel University, Philadelphia, US","institution_ids":["https://openalex.org/I72816309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101569679","display_name":"Xiaohua Hu","orcid":"https://orcid.org/0000-0002-4777-3022"},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaohua Hu","raw_affiliation_strings":["College of Computing and Informatics, Drexel University, Philadelphia, US"],"affiliations":[{"raw_affiliation_string":"College of Computing and Informatics, Drexel University, Philadelphia, US","institution_ids":["https://openalex.org/I72816309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016398897","display_name":"Ahmet Sa\u00e7an","orcid":"https://orcid.org/0000-0002-3570-3270"},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ahmet Sacan","raw_affiliation_strings":["School of Biomedical Engineering, Science and Health Systems Drexel University, Philadelphia, US"],"affiliations":[{"raw_affiliation_string":"School of Biomedical Engineering, Science and Health Systems Drexel University, Philadelphia, US","institution_ids":["https://openalex.org/I72816309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5101571739"],"corresponding_institution_ids":["https://openalex.org/I1335321130"],"apc_list":null,"apc_paid":null,"fwci":0.2127,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.55156333,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"97","last_page":"100"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987999796867371,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987999796867371,"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":0.9902999997138977,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9876000285148621,"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/support-vector-machine","display_name":"Support vector machine","score":0.7747548818588257},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6395898461341858},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6296560764312744},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5866870284080505},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.5032364726066589},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4969952404499054},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.4835500419139862},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4824241101741791},{"id":"https://openalex.org/keywords/human-proteins","display_name":"Human proteins","score":0.46887922286987305},{"id":"https://openalex.org/keywords/structural-similarity","display_name":"Structural similarity","score":0.4437437951564789},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4381124973297119},{"id":"https://openalex.org/keywords/structural-alignment","display_name":"Structural alignment","score":0.4377235174179077},{"id":"https://openalex.org/keywords/human-immunodeficiency-virus","display_name":"Human immunodeficiency virus (HIV)","score":0.43308234214782715},{"id":"https://openalex.org/keywords/kernel-method","display_name":"Kernel method","score":0.41046085953712463},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38002169132232666},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21370390057563782},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.150541752576828},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1341552734375},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12484753131866455},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1153915524482727},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.09076195955276489}],"concepts":[{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.7747548818588257},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6395898461341858},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6296560764312744},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5866870284080505},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.5032364726066589},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4969952404499054},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.4835500419139862},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4824241101741791},{"id":"https://openalex.org/C2911029443","wikidata":"https://www.wikidata.org/wiki/Q21296145","display_name":"Human proteins","level":3,"score":0.46887922286987305},{"id":"https://openalex.org/C139489369","wikidata":"https://www.wikidata.org/wiki/Q770846","display_name":"Structural similarity","level":2,"score":0.4437437951564789},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4381124973297119},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.4377235174179077},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.43308234214782715},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.41046085953712463},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38002169132232666},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21370390057563782},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.150541752576828},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1341552734375},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12484753131866455},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1153915524482727},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.09076195955276489},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2017.8217632","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2017.8217632","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.44999998807907104,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W82851467","https://openalex.org/W1966546784","https://openalex.org/W1969327849","https://openalex.org/W1979237722","https://openalex.org/W2021703339","https://openalex.org/W2032718703","https://openalex.org/W2071099150","https://openalex.org/W2071115911","https://openalex.org/W2077398039","https://openalex.org/W2105476170","https://openalex.org/W2130687290","https://openalex.org/W2155723007","https://openalex.org/W2158945625","https://openalex.org/W2161062388","https://openalex.org/W2162388472","https://openalex.org/W2275032899","https://openalex.org/W6658514094","https://openalex.org/W6669829439"],"related_works":["https://openalex.org/W2073953701","https://openalex.org/W98859716","https://openalex.org/W2084367350","https://openalex.org/W2121593618","https://openalex.org/W2740792986","https://openalex.org/W2279605073","https://openalex.org/W2026882519","https://openalex.org/W2014499409","https://openalex.org/W2593283542","https://openalex.org/W2547795274"],"abstract_inverted_index":{"In":[0],"this":[1],"paper,":[2],"we":[3,54,115],"computationally":[4],"predicted":[5,108],"the":[6,15,39,76,91,117,131],"interactions":[7,52,109],"between":[8,41],"HIV-1":[9,101,123],"and":[10,93,114,126],"human":[11,50,105],"proteins,":[12],"based":[13],"on":[14],"hypothesis":[16],"that":[17],"proteins":[18],"with":[19,72],"similar":[20,24],"interface":[21,44],"architecture":[22],"share":[23],"interaction":[25],"partners.":[26],"Evolution":[27],"-":[28],"aware":[29],"protein":[30,43,83],"structural":[31,133],"alignment":[32],"method":[33],"UniAlign":[34],"was":[35],"used":[36,90],"to":[37,97],"calculate":[38],"similarity":[40,63],"two":[42],"architectures.":[45],"Using":[46],"experimentally":[47],"verified":[48],"HIV-1,":[49],"protein-protein":[51],"data,":[53],"first":[55,132],"selected":[56],"12":[57],"features,":[58],"including":[59],"geometric":[60],"similarity,":[61],"conversion":[62],"etc.;":[64],"then":[65],"trained":[66,92],"a":[67,81],"support":[68],"vector":[69],"machine":[70],"(SVM)":[71],"Gaussian":[73],"kernel":[74],"for":[75,104,122,135],"binary":[77],"classification":[78],"problem:":[79],"whether":[80],"given":[82],"pairs":[84],"`interact'":[85],"or":[86],"`no":[87],"interact'.":[88],"We":[89,129],"tuned":[94],"SVM":[95],"classifier":[96],"discover":[98],"potential":[99],"novel":[100,118],"interacting":[102,120],"partners":[103],"proteins.":[106,128],"Many":[107],"had":[110],"significant":[111],"literature":[112],"support,":[113],"modeled":[116],"3D":[119],"complex":[121],"envelope":[124],"gp120":[125],"gp41":[127],"provided":[130],"evidence":[134],"those":[136],"interactions.":[137]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-25T21:42:39.735039","created_date":"2025-10-10T00:00:00"}