{"id":"https://openalex.org/W2052097062","doi":"https://doi.org/10.1093/nar/gkj032","title":"VIPERdb: a relational database for structural virology","display_name":"VIPERdb: a relational database for structural virology","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W2052097062","doi":"https://doi.org/10.1093/nar/gkj032","mag":"2052097062","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381893"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj032","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj032","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D386/3923840/gkj032.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D386/3923840/gkj032.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084499425","display_name":"Craig M. Shepherd","orcid":null},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"C. M. Shepherd","raw_affiliation_strings":["Department of Molecular Biology, TPC-6 The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, TPC-6 The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I123431417"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5084499425"],"corresponding_institution_ids":["https://openalex.org/I123431417"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":18.5536,"has_fulltext":false,"cited_by_count":125,"citation_normalized_percentile":{"value":0.99643041,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"34","issue":"90001","first_page":"D386","last_page":"D389"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9941999912261963,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10340","display_name":"Hepatitis B Virus Studies","score":0.993399977684021,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6656326055526733},{"id":"https://openalex.org/keywords/capsid","display_name":"Capsid","score":0.6318470239639282},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.6021202802658081},{"id":"https://openalex.org/keywords/icosahedral-symmetry","display_name":"Icosahedral symmetry","score":0.491970032453537},{"id":"https://openalex.org/keywords/structural-bioinformatics","display_name":"Structural bioinformatics","score":0.4807450771331787},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.46794620156288147},{"id":"https://openalex.org/keywords/uniprot","display_name":"UniProt","score":0.4419369101524353},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4317989945411682},{"id":"https://openalex.org/keywords/schema","display_name":"Schema (genetic algorithms)","score":0.43049055337905884},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3952782452106476},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.36201009154319763},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.28075501322746277},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.20505735278129578},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.152099609375},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.13419121503829956},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09490445256233215},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.0734579861164093}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6656326055526733},{"id":"https://openalex.org/C202878990","wikidata":"https://www.wikidata.org/wiki/Q830465","display_name":"Capsid","level":3,"score":0.6318470239639282},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.6021202802658081},{"id":"https://openalex.org/C113709186","wikidata":"https://www.wikidata.org/wiki/Q5986738","display_name":"Icosahedral symmetry","level":2,"score":0.491970032453537},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.4807450771331787},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.46794620156288147},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.4419369101524353},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4317989945411682},{"id":"https://openalex.org/C52146309","wikidata":"https://www.wikidata.org/wiki/Q7431116","display_name":"Schema (genetic algorithms)","level":2,"score":0.43049055337905884},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3952782452106476},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.36201009154319763},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.28075501322746277},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.20505735278129578},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.152099609375},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.13419121503829956},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09490445256233215},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.0734579861164093},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002213","descriptor_name":"Capsid","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D002213","descriptor_name":"Capsid","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D002213","descriptor_name":"Capsid","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D002213","descriptor_name":"Capsid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002213","descriptor_name":"Capsid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002213","descriptor_name":"Capsid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D036022","descriptor_name":"Capsid Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkj032","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj032","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D386/3923840/gkj032.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16381893","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381893","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:1347395","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347395","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkj032","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj032","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D386/3923840/gkj032.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5099999904632568,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2052097062.pdf","grobid_xml":"https://content.openalex.org/works/W2052097062.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1965501120","https://openalex.org/W1987688066","https://openalex.org/W2024563987","https://openalex.org/W2025807241","https://openalex.org/W2028231353","https://openalex.org/W2040206116","https://openalex.org/W2059284454","https://openalex.org/W2078507839","https://openalex.org/W2083334314","https://openalex.org/W2090595596","https://openalex.org/W2097671740","https://openalex.org/W2104290891","https://openalex.org/W2132629607"],"related_works":["https://openalex.org/W1665067482","https://openalex.org/W2103435205","https://openalex.org/W2465617737","https://openalex.org/W4387823862","https://openalex.org/W2559289600","https://openalex.org/W4230842383","https://openalex.org/W2097016219","https://openalex.org/W4375844720","https://openalex.org/W2123480822","https://openalex.org/W2978232173"],"abstract_inverted_index":{"VIPERdb":[0],"(http://viperdb.scripps.edu)":[1],"is":[2,12],"a":[3,15,51],"database":[4,47],"for":[5,53,120],"icosahedral":[6],"virus":[7,86],"capsid":[8],"structures.":[9],"Our":[10],"aim":[11],"to":[13,19,61,104,111],"provide":[14],"comprehensive":[16],"resource":[17],"specific":[18],"the":[20,23,31,57,62,68,96],"needs":[21],"of":[22,35,43,85],"structural":[24,39,82,100],"virology":[25],"community,":[26],"with":[27,72],"an":[28],"emphasis":[29],"on":[30,50,95],"description":[32],"and":[33,40,92,101,108,115],"comparison":[34],"derived":[36,102],"data":[37,58,77,103],"from":[38],"energetic":[41],"analyses":[42],"capsids.":[44,87],"A":[45],"relational":[46],"implementation":[48],"based":[49],"schema":[52],"macromolecular":[54],"structure":[55],"makes":[56],"highly":[59],"accessible":[60],"user,":[63],"allowing":[64],"detailed":[65],"queries":[66],"at":[67],"atomic":[69],"level.":[70],"Together":[71],"curation":[73],"practices":[74],"that":[75],"maintain":[76],"uniformity,":[78],"this":[79],"will":[80],"facilitate":[81],"bioinformatics":[83],"studies":[84],"User":[88],"friendly":[89],"search,":[90],"visualization":[91],"educational":[93],"tools":[94],"website":[97],"allow":[98],"both":[99],"be":[105],"examined":[106],"easily":[107],"extensively.":[109],"Links":[110],"relevant":[112],"literature,":[113],"sequence":[114],"taxonomy":[116],"databases":[117],"are":[118],"provided":[119],"each":[121],"entry.":[122]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":5}],"updated_date":"2026-03-17T09:09:15.849793","created_date":"2025-10-10T00:00:00"}
