{"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"},"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"],"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"],"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"],"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"],"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":3,"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":0.1545,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.51139366,"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":[],"locations_count":2,"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":"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":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.7799999713897705}],"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":{"pdf":true,"grobid_xml":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":{"Abstract":[0],"Epitope":[1],"residues":[2],"located":[3],"on":[4,29,57,219],"viral":[5,58,74,184,220],"surface":[6,59],"proteins":[7],"are":[8,170,231],"of":[9,37,48,55,77,81,120,152,174,191,204],"immense":[10],"interest":[11],"in":[12,40,138,198],"immunology":[13],"and":[14,23,46,85,116,131,156,161,176,195,216,228],"related":[15],"applications":[16],"such":[17,33,107,123],"as":[18,34,108,111,113,124,206],"vaccine":[19],"development,":[20],"disease":[21],"diagnosis":[22],"drug":[24],"design.":[25],"Most":[26],"tools":[27],"rely":[28],"sequence-based":[30],"statistical":[31],"comparisons,":[32],"information":[35],"entropy":[36],"residue":[38,114,129],"positions":[39],"aligned":[41],"columns":[42],"to":[43],"infer":[44],"location":[45],"properties":[47,93,122,188],"epitope":[49,83,91,154],"sites.":[50],"To":[51,143],"facilitate":[52,214],"cross-structural":[53],"comparisons":[54],"epitopes":[56,173,221],"proteins,":[60],"a":[61,73,79,86,118,150],"python-based":[62],"extraction":[63],"tool":[64,99,212],"implemented":[65],"with":[66,208],"Jupyter":[67],"notebook":[68],"is":[69],"presented":[70],"(Jupytope).":[71],"Given":[72],"antigen":[75],"structure":[76,133,160],"interest,":[78],"list":[80,119,151],"known":[82],"sites":[84,155],"reference":[87,159],"structure,":[88],"the":[89,166,223],"corresponding":[90,158],"structural":[92,225],"can":[94,135],"quickly":[95],"be":[96,136],"obtained.":[97],"The":[98,186,211],"integrates":[100],"biopython":[101],"modules":[102],"for":[103,172],"commonly":[104],"used":[105],"software":[106],"NACCESS,":[109],"DSSP":[110],"well":[112],"depth":[115,130],"outputs":[117],"structure-derived":[121],"dihedral":[125],"angles,":[126],"solvent":[127],"accessibility,":[128],"secondary":[132],"that":[134],"saved":[137],"several":[139],"convenient":[140],"data":[141],"formats.":[142],"ensure":[144],"correct":[145],"spatial":[146],"alignment,":[147],"Jupytope":[148,227],"takes":[149],"given":[153],"their":[157],"aligns":[162],"them":[163],"before":[164],"extracting":[165],"desired":[167],"properties.":[168],"Examples":[169],"demonstrated":[171],"Influenza":[175,193],"severe":[177],"acute":[178],"respiratory":[179],"syndrome":[180],"coronavirus":[181],"2":[182],"(SARS-CoV2)":[183],"strains.":[185],"extracted":[187,224,229],"assist":[189],"detection":[190],"two":[192],"subtypes":[194],"show":[196],"potential":[197],"distinguishing":[199],"between":[200],"four":[201],"major":[202],"clades":[203],"SARS-CoV2,":[205],"compared":[207],"randomized":[209],"labels.":[210],"will":[213],"analytical":[215],"predictive":[217],"works":[218],"through":[222],"information.":[226],"datasets":[230],"available":[232],"at":[233],"https://github.com/shamimarashid/Jupytope.":[234]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2022-09-12T00:00:00"}
