{"id":"https://openalex.org/W4225009860","doi":"https://doi.org/10.1093/nar/gkac279","title":"GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents","display_name":"GraPES: The Granule Protein Enrichment Server for prediction of biological condensate constituents","publication_year":2022,"publication_date":"2022-04-14","ids":{"openalex":"https://openalex.org/W4225009860","doi":"https://doi.org/10.1093/nar/gkac279","pmid":"https://pubmed.ncbi.nlm.nih.gov/35474477"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkac279","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac279","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W384/44378406/gkac279.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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/50/W1/W384/44378406/gkac279.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010199730","display_name":"Erich R. Kuechler","orcid":"https://orcid.org/0000-0002-4733-7554"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Erich R Kuechler","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia , Vancouver , BC , Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia , Vancouver , BC , Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001224002","display_name":"Matthew P. Jacobson","orcid":"https://orcid.org/0000-0001-6262-655X"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Matthew Jacobson","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia , Vancouver , BC , Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia , Vancouver , BC , Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046029600","display_name":"Thibault Mayor","orcid":"https://orcid.org/0000-0002-9289-3939"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Thibault Mayor","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia , Vancouver , BC , Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia , Vancouver , BC , Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011423412","display_name":"J\u00f6rg Gsponer","orcid":"https://orcid.org/0000-0003-3672-6594"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210133112","display_name":"Canada's Michael Smith Genome Sciences Centre","ror":"https://ror.org/0333j0897","country_code":"CA","type":"other","lineage":["https://openalex.org/I4210133112"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"J\u00f6rg Gsponer","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia , Vancouver , BC , Canada"],"raw_orcid":"https://orcid.org/0000-0003-3672-6594","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia , Vancouver , BC , Canada","institution_ids":["https://openalex.org/I4210133112","https://openalex.org/I141945490"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5011423412"],"corresponding_institution_ids":["https://openalex.org/I141945490","https://openalex.org/I4210133112"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.4755,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.81565888,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"50","issue":"W1","first_page":"W384","last_page":"W391"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9994000196456909,"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/T10604","display_name":"RNA Research and Splicing","score":0.9994000196456909,"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/T11482","display_name":"RNA modifications and cancer","score":0.9990000128746033,"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/T13157","display_name":"Cancer-related gene regulation","score":0.9979000091552734,"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/biology","display_name":"Biology","score":0.9263083934783936},{"id":"https://openalex.org/keywords/granule","display_name":"Granule (geology)","score":0.5625942945480347},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4217790365219116},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.373239129781723}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9263083934783936},{"id":"https://openalex.org/C49760210","wikidata":"https://www.wikidata.org/wiki/Q5596727","display_name":"Granule (geology)","level":2,"score":0.5625942945480347},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4217790365219116},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.373239129781723},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000088162","descriptor_name":"Stress Granules","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000088162","descriptor_name":"Stress Granules","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000088162","descriptor_name":"Stress Granules","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000088162","descriptor_name":"Stress Granules","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000088162","descriptor_name":"Stress Granules","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000088162","descriptor_name":"Stress Granules","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003201","descriptor_name":"Computers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006360","descriptor_name":"Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006360","descriptor_name":"Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006360","descriptor_name":"Heat-Shock Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D012261","descriptor_name":"Ribonucleoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012261","descriptor_name":"Ribonucleoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012261","descriptor_name":"Ribonucleoproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012261","descriptor_name":"Ribonucleoproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012261","descriptor_name":"Ribonucleoproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012261","descriptor_name":"Ribonucleoproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015388","descriptor_name":"Organelles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015388","descriptor_name":"Organelles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015388","descriptor_name":"Organelles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkac279","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac279","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W384/44378406/gkac279.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:35474477","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35474477","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:9252806","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9252806","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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/gkac279","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkac279","pdf_url":"https://academic.oup.com/nar/article-pdf/50/W1/W384/44378406/gkac279.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5255600770","display_name":null,"funder_award_id":"PJT-175104","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G5954498218","display_name":null,"funder_award_id":"PJT-148489","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"}],"funders":[{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4225009860.pdf","grobid_xml":"https://content.openalex.org/works/W4225009860.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1894813487","https://openalex.org/W1912455695","https://openalex.org/W1962225963","https://openalex.org/W1975304761","https://openalex.org/W1991140361","https://openalex.org/W2027839322","https://openalex.org/W2043274355","https://openalex.org/W2064295826","https://openalex.org/W2097606916","https://openalex.org/W2103083136","https://openalex.org/W2138267133","https://openalex.org/W2144216698","https://openalex.org/W2153114644","https://openalex.org/W2162980545","https://openalex.org/W2173751674","https://openalex.org/W2182726182","https://openalex.org/W2425405879","https://openalex.org/W2508376386","https://openalex.org/W2561871078","https://openalex.org/W2573507107","https://openalex.org/W2590568317","https://openalex.org/W2593862218","https://openalex.org/W2784370070","https://openalex.org/W2784401093","https://openalex.org/W2786469974","https://openalex.org/W2792650153","https://openalex.org/W2794654572","https://openalex.org/W2801412154","https://openalex.org/W2900206619","https://openalex.org/W2901765635","https://openalex.org/W2903887467","https://openalex.org/W2929462375","https://openalex.org/W2938155522","https://openalex.org/W2969279439","https://openalex.org/W2980567099","https://openalex.org/W2991067665","https://openalex.org/W2997051198","https://openalex.org/W3008140494","https://openalex.org/W3033583915","https://openalex.org/W3092508309","https://openalex.org/W3128708278","https://openalex.org/W3136918052","https://openalex.org/W3148151718"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"Phase":[0],"separation-based":[1],"condensate":[2],"formation":[3],"is":[4,94,101,108],"a":[5,32,49],"novel":[6],"working":[7],"paradigm":[8],"in":[9,103],"biology,":[10],"helping":[11],"to":[12],"rationalize":[13],"many":[14],"important":[15],"cellular":[16,29,67],"phenomena":[17],"including":[18],"the":[19,25,42,54,119,133],"assembly":[20],"of":[21,28,35,123],"membraneless":[22],"organelles.":[23],"Uncovering":[24],"functional":[26],"impact":[27],"condensates":[30],"requires":[31],"better":[33],"knowledge":[34],"these":[36],"condensates'":[37],"constituents.":[38],"Herein,":[39],"we":[40],"introduce":[41],"webserver":[43],"GraPES":[44,100],"(Granule":[45],"Protein":[46],"Enrichment":[47],"Server),":[48],"user-friendly":[50],"online":[51],"interface":[52],"containing":[53],"MaGS":[55,85],"and":[56,78,105,107,126],"MaGSeq":[57,93],"predictors,":[58],"which":[59],"provide":[60],"propensity":[61],"scores":[62],"for":[63,90,111,117],"proteins'":[64],"localization":[65],"into":[66],"condensates.":[68],"Our":[69],"webpage":[70],"contains":[71],"models":[72],"trained":[73],"on":[74,132],"human":[75],"(Homo":[76],"sapiens)":[77],"yeast":[79],"(Saccharomyces":[80],"cerevisiae)":[81],"stress":[82],"granule":[83],"proteins.":[84],"utilizes":[86],"experimentally-based":[87],"protein":[88,97],"features":[89],"prediction,":[91],"whereas":[92],"an":[95],"entirely":[96],"sequence-based":[98],"implementation.":[99],"implemented":[102],"HTML/CSS":[104],"Javascript":[106],"freely":[109],"available":[110],"public":[112],"use":[113],"at":[114],"https://grapes.msl.ubc.ca/.":[115],"Documentation":[116],"using":[118],"provided":[120],"webtools,":[121],"descriptions":[122],"their":[124],"methodology,":[125],"implementation":[127],"notes":[128],"can":[129],"be":[130],"found":[131],"webpage.":[134]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
