{"id":"https://openalex.org/W4295242189","doi":"https://doi.org/10.1093/bib/bbac362","title":"Jupytope: computational extraction of structural properties of viral epitopes","display_name":"Jupytope: computational extraction of structural properties of viral epitopes","publication_year":2022,"publication_date":"2022-09-08","ids":{"openalex":"https://openalex.org/W4295242189","doi":"https://doi.org/10.1093/bib/bbac362","pmid":"https://pubmed.ncbi.nlm.nih.gov/36094101"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac362","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbac362/45799407/bbac362.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbac362/45799407/bbac362.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037891222","display_name":"Shamima Rashid","orcid":"https://orcid.org/0000-0002-0157-6525"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Shamima Rashid","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798 , Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798 , Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000728220","display_name":"Teng Ann Ng","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Teng Ann Ng","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798 , Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798 , Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027208445","display_name":"Chee Keong Kwoh","orcid":"https://orcid.org/0000-0002-8547-6387"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Chee Keong Kwoh","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798 , Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798 , Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5027208445"],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.154,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.50730393,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"23","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9995999932289124,"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":0.9995999932289124,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9995999932289124,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976000189781189,"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/epitope","display_name":"Epitope","score":0.9462299942970276},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.606386661529541},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5935779809951782},{"id":"https://openalex.org/keywords/residue","display_name":"Residue (chemistry)","score":0.432540625333786},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4160923361778259},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.32216769456863403},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3004217743873596},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.237682044506073},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11256447434425354},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.07961413264274597}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.9462299942970276},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.606386661529541},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5935779809951782},{"id":"https://openalex.org/C2781338088","wikidata":"https://www.wikidata.org/wiki/Q903495","display_name":"Residue (chemistry)","level":2,"score":0.432540625333786},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4160923361778259},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.32216769456863403},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3004217743873596},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.237682044506073},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11256447434425354},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.07961413264274597}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008565","descriptor_name":"Membrane Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbac362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac362","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbac362/45799407/bbac362.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36094101","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36094101","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:dr.ntu.edu.sg:10356/178480","is_oa":false,"landing_page_url":"https://hdl.handle.net/10356/178480","pdf_url":null,"source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbac362","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac362","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbac362/45799407/bbac362.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7799999713897705,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G6566187743","display_name":null,"funder_award_id":"MOE2020-T1-001-130","funder_id":"https://openalex.org/F4320327296","funder_display_name":"Ministry of Education \u2013 Kingdom of Saudi Arabi"},{"id":"https://openalex.org/G866528241","display_name":null,"funder_award_id":"MOE2019-T2-2-175","funder_id":"https://openalex.org/F4320327296","funder_display_name":"Ministry of Education \u2013 Kingdom of Saudi Arabi"}],"funders":[{"id":"https://openalex.org/F4320322724","display_name":"Ministry of Education, India","ror":"https://ror.org/048xjjh50"},{"id":"https://openalex.org/F4320327296","display_name":"Ministry of Education \u2013 Kingdom of Saudi Arabi","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4295242189.pdf","grobid_xml":"https://content.openalex.org/works/W4295242189.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W86407692","https://openalex.org/W1975304761","https://openalex.org/W1983113740","https://openalex.org/W2008708467","https://openalex.org/W2100316154","https://openalex.org/W2100908214","https://openalex.org/W2119611042","https://openalex.org/W2121731372","https://openalex.org/W2123156966","https://openalex.org/W2130479394","https://openalex.org/W2142678478","https://openalex.org/W2156260957","https://openalex.org/W2158886341","https://openalex.org/W2158899863","https://openalex.org/W2414582588","https://openalex.org/W2502066314","https://openalex.org/W2518750490","https://openalex.org/W2525128349","https://openalex.org/W2559927678","https://openalex.org/W2742180939","https://openalex.org/W2890790004","https://openalex.org/W2892089013","https://openalex.org/W2894631181","https://openalex.org/W2899053251","https://openalex.org/W2906578344","https://openalex.org/W2917097596","https://openalex.org/W2971835553","https://openalex.org/W2980467043","https://openalex.org/W3003415212","https://openalex.org/W3004318991","https://openalex.org/W3016143592","https://openalex.org/W3021559842","https://openalex.org/W3035265089","https://openalex.org/W3043124965","https://openalex.org/W3046463683","https://openalex.org/W3047569588","https://openalex.org/W3048525157","https://openalex.org/W3048794251","https://openalex.org/W3118810627","https://openalex.org/W3119250802","https://openalex.org/W3140076283","https://openalex.org/W3150505176","https://openalex.org/W3157447802","https://openalex.org/W3201551509","https://openalex.org/W3208048420","https://openalex.org/W4200283880","https://openalex.org/W4205478771","https://openalex.org/W4210671226","https://openalex.org/W4220856915","https://openalex.org/W4255659575","https://openalex.org/W4293003482"],"related_works":["https://openalex.org/W1979044599","https://openalex.org/W2021824670","https://openalex.org/W2009867644","https://openalex.org/W2363997565","https://openalex.org/W1981120125","https://openalex.org/W3036615648","https://openalex.org/W2408448169","https://openalex.org/W2182598264","https://openalex.org/W2075879923","https://openalex.org/W2205639271"],"abstract_inverted_index":{"Epitope":[0],"residues":[1],"located":[2],"on":[3,28,56,218],"viral":[4,57,73,183,219],"surface":[5,58],"proteins":[6],"are":[7,169,230],"of":[8,36,47,54,76,80,119,151,173,190,203],"immense":[9],"interest":[10],"in":[11,39,137,197],"immunology":[12],"and":[13,22,45,84,115,130,155,160,175,194,215,227],"related":[14],"applications":[15],"such":[16,32,106,122],"as":[17,33,107,110,112,123,205],"vaccine":[18],"development,":[19],"disease":[20],"diagnosis":[21],"drug":[23],"design.":[24],"Most":[25],"tools":[26],"rely":[27],"sequence-based":[29],"statistical":[30],"comparisons,":[31],"information":[34],"entropy":[35],"residue":[37,113,128],"positions":[38],"aligned":[40],"columns":[41],"to":[42],"infer":[43],"location":[44],"properties":[46,92,121,187],"epitope":[48,82,90,153],"sites.":[49],"To":[50,142],"facilitate":[51,213],"cross-structural":[52],"comparisons":[53],"epitopes":[55,172,220],"proteins,":[59],"a":[60,72,78,85,117,149],"python-based":[61],"extraction":[62],"tool":[63,98,211],"implemented":[64],"with":[65,207],"Jupyter":[66],"notebook":[67],"is":[68],"presented":[69],"(Jupytope).":[70],"Given":[71],"antigen":[74],"structure":[75,132,159],"interest,":[77],"list":[79,118,150],"known":[81],"sites":[83,154],"reference":[86,158],"structure,":[87],"the":[88,165,222],"corresponding":[89,157],"structural":[91,224],"can":[93,134],"quickly":[94],"be":[95,135],"obtained.":[96],"The":[97,185,210],"integrates":[99],"biopython":[100],"modules":[101],"for":[102,171],"commonly":[103],"used":[104],"software":[105],"NACCESS,":[108],"DSSP":[109],"well":[111],"depth":[114,129],"outputs":[116],"structure-derived":[120],"dihedral":[124],"angles,":[125],"solvent":[126],"accessibility,":[127],"secondary":[131],"that":[133],"saved":[136],"several":[138],"convenient":[139],"data":[140],"formats.":[141],"ensure":[143],"correct":[144],"spatial":[145],"alignment,":[146],"Jupytope":[147,226],"takes":[148],"given":[152],"their":[156],"aligns":[161],"them":[162],"before":[163],"extracting":[164],"desired":[166],"properties.":[167],"Examples":[168],"demonstrated":[170],"Influenza":[174,192],"severe":[176],"acute":[177],"respiratory":[178],"syndrome":[179],"coronavirus":[180],"2":[181],"(SARS-CoV2)":[182],"strains.":[184],"extracted":[186,223,228],"assist":[188],"detection":[189],"two":[191],"subtypes":[193],"show":[195],"potential":[196],"distinguishing":[198],"between":[199],"four":[200],"major":[201],"clades":[202],"SARS-CoV2,":[204],"compared":[206],"randomized":[208],"labels.":[209],"will":[212],"analytical":[214],"predictive":[216],"works":[217],"through":[221],"information.":[225],"datasets":[229],"available":[231],"at":[232],"https://github.com/shamimarashid/Jupytope.":[233]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2022-09-12T00:00:00"}