{"id":"https://openalex.org/W2024405748","doi":"https://doi.org/10.1093/bioinformatics/btv195","title":"PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels","display_name":"PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels","publication_year":2015,"publication_date":"2015-04-06","ids":{"openalex":"https://openalex.org/W2024405748","doi":"https://doi.org/10.1093/bioinformatics/btv195","mag":"2024405748","pmid":"https://pubmed.ncbi.nlm.nih.gov/25851949"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv195","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv195","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/16/2745/49035314/bioinformatics_31_16_2745.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/article-pdf/31/16/2745/49035314/bioinformatics_31_16_2745.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023771318","display_name":"Yongwook Choi","orcid":"https://orcid.org/0000-0003-4017-9669"},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yongwook Choi","raw_affiliation_strings":["The J. Craig Venter Institute, Rockville, MD 20850, USA","The J, Craig Venter Institute, Rockville, MD 20850, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The J. Craig Venter Institute, Rockville, MD 20850, USA","institution_ids":["https://openalex.org/I1301553790"]},{"raw_affiliation_string":"The J, Craig Venter Institute, Rockville, MD 20850, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005001979","display_name":"Agnes P. Chan","orcid":"https://orcid.org/0000-0003-2373-9580"},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Agnes P. Chan","raw_affiliation_strings":["The J. Craig Venter Institute, Rockville, MD 20850, USA","The J, Craig Venter Institute, Rockville, MD 20850, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The J. Craig Venter Institute, Rockville, MD 20850, USA","institution_ids":["https://openalex.org/I1301553790"]},{"raw_affiliation_string":"The J, Craig Venter Institute, Rockville, MD 20850, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5023771318"],"corresponding_institution_ids":["https://openalex.org/I1301553790"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":93.7019,"has_fulltext":true,"cited_by_count":2639,"citation_normalized_percentile":{"value":0.99964972,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"31","issue":"16","first_page":"2745","last_page":"2747"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.8913000226020813,"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"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.8913000226020813,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.019999999552965164,"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":0.014800000004470348,"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/web-server","display_name":"Web server","score":0.7564483880996704},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.740872859954834},{"id":"https://openalex.org/keywords/login","display_name":"Login","score":0.6754153370857239},{"id":"https://openalex.org/keywords/indel","display_name":"Indel","score":0.6202462911605835},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5153400301933289},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3723427355289459},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3423907160758972},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.31493258476257324},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.26635223627090454},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.256222128868103},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.24580121040344238},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14268144965171814},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.0863569974899292}],"concepts":[{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.7564483880996704},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.740872859954834},{"id":"https://openalex.org/C113324615","wikidata":"https://www.wikidata.org/wiki/Q472302","display_name":"Login","level":2,"score":0.6754153370857239},{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.6202462911605835},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5153400301933289},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3723427355289459},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3423907160758972},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.31493258476257324},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.26635223627090454},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.256222128868103},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.24580121040344238},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14268144965171814},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.0863569974899292},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017384","descriptor_name":"Sequence Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017384","descriptor_name":"Sequence Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017384","descriptor_name":"Sequence Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019943","descriptor_name":"Amino Acid Substitution","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv195","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv195","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/16/2745/49035314/bioinformatics_31_16_2745.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25851949","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25851949","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:3944664","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4528627","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/16/2745","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/16/2745","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv195","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv195","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/16/2745/49035314/bioinformatics_31_16_2745.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.4399999976158142,"id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2024405748.pdf","grobid_xml":"https://content.openalex.org/works/W2024405748.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W1980740976","https://openalex.org/W2034528478","https://openalex.org/W2054185647","https://openalex.org/W2059145105","https://openalex.org/W2089335658","https://openalex.org/W2127981150","https://openalex.org/W2164004777","https://openalex.org/W2167257571"],"related_works":["https://openalex.org/W2033001683","https://openalex.org/W4256170434","https://openalex.org/W2046457574","https://openalex.org/W2167094946","https://openalex.org/W4235220108","https://openalex.org/W4315650027","https://openalex.org/W4285059642","https://openalex.org/W4382398022","https://openalex.org/W1949458596","https://openalex.org/W3144677376"],"abstract_inverted_index":{"UNLABELLED:":[0],"We":[1],"present":[2],"a":[3],"web":[4,58],"server":[5,27,59],"to":[6,65],"predict":[7],"the":[8,22,49],"functional":[9],"effect":[10],"of":[11,31],"single":[12],"or":[13],"multiple":[14],"amino":[15],"acid":[16],"substitutions,":[17],"insertions":[18],"and":[19,37,44,51,63],"deletions":[20],"using":[21],"prediction":[23],"tool":[24],"PROVEAN.":[25],"The":[26,57],"provides":[28],"rapid":[29],"analysis":[30,41],"protein":[32,52],"variants":[33,46],"from":[34],"any":[35],"organisms,":[36],"also":[38],"supports":[39],"high-throughput":[40],"for":[42],"human":[43],"mouse":[45],"at":[47,72,82],"both":[48],"genomic":[50],"levels.":[53],"AVAILABILITY":[54],"AND":[55],"IMPLEMENTATION:":[56],"is":[60],"freely":[61],"available":[62,81],"open":[64],"all":[66],"users":[67],"with":[68],"no":[69],"login":[70],"requirements":[71],"http://provean.jcvi.org.":[73],"CONTACT:":[74],"achan@jcvi.org":[75],"SUPPLEMENTARY":[76],"INFORMATION:":[77],"Supplementary":[78],"data":[79],"are":[80],"Bioinformatics":[83],"online.":[84]},"counts_by_year":[{"year":2026,"cited_by_count":51},{"year":2025,"cited_by_count":186},{"year":2024,"cited_by_count":225},{"year":2023,"cited_by_count":324},{"year":2022,"cited_by_count":380},{"year":2021,"cited_by_count":485},{"year":2020,"cited_by_count":348},{"year":2019,"cited_by_count":250},{"year":2018,"cited_by_count":158},{"year":2017,"cited_by_count":126},{"year":2016,"cited_by_count":86},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-11T08:15:01.531666","created_date":"2025-10-10T00:00:00"}
