{"id":"https://openalex.org/W2806774184","doi":"https://doi.org/10.1093/bioinformatics/bty434","title":"An <i>in silico</i> proteomics screen to predict and prioritize protein\u2013protein interactions dependent on post-translationally modified motifs","display_name":"An <i>in silico</i> proteomics screen to predict and prioritize protein\u2013protein interactions dependent on post-translationally modified motifs","publication_year":2018,"publication_date":"2018-05-25","ids":{"openalex":"https://openalex.org/W2806774184","doi":"https://doi.org/10.1093/bioinformatics/bty434","mag":"2806774184","pmid":"https://pubmed.ncbi.nlm.nih.gov/29868839"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty434","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty434","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/22/3898/26441449/bty434.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/34/22/3898/26441449/bty434.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067737318","display_name":"Anna M. Schmoker","orcid":"https://orcid.org/0000-0003-2830-5650"},"institutions":[{"id":"https://openalex.org/I111236770","display_name":"University of Vermont","ror":"https://ror.org/0155zta11","country_code":"US","type":"education","lineage":["https://openalex.org/I111236770"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anna M Schmoker","raw_affiliation_strings":["Department of Biology, University of Vermont, Burlington, VT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Vermont, Burlington, VT, USA","institution_ids":["https://openalex.org/I111236770"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009502020","display_name":"Heather Driscoll","orcid":"https://orcid.org/0000-0002-3772-9933"},"institutions":[{"id":"https://openalex.org/I4210088533","display_name":"Vermont Oxford Network","ror":"https://ror.org/003gt3k37","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210088533"]},{"id":"https://openalex.org/I169768744","display_name":"Norwich University","ror":"https://ror.org/04we7d902","country_code":"US","type":"education","lineage":["https://openalex.org/I169768744"]},{"id":"https://openalex.org/I111236770","display_name":"University of Vermont","ror":"https://ror.org/0155zta11","country_code":"US","type":"education","lineage":["https://openalex.org/I111236770"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heather E Driscoll","raw_affiliation_strings":["Department of Biology, Norwich University, Northfield, VT, USA","Vermont Genetics Network Bioinformatics Core, University of Vermont, Burlington, VT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Norwich University, Northfield, VT, USA","institution_ids":["https://openalex.org/I169768744"]},{"raw_affiliation_string":"Vermont Genetics Network Bioinformatics Core, University of Vermont, Burlington, VT, USA","institution_ids":["https://openalex.org/I4210088533","https://openalex.org/I111236770"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059881643","display_name":"Stefanie R Geiger","orcid":null},"institutions":[{"id":"https://openalex.org/I111236770","display_name":"University of Vermont","ror":"https://ror.org/0155zta11","country_code":"US","type":"education","lineage":["https://openalex.org/I111236770"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stefanie R Geiger","raw_affiliation_strings":["Department of Biology, University of Vermont, Burlington, VT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Vermont, Burlington, VT, USA","institution_ids":["https://openalex.org/I111236770"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009494974","display_name":"James J. Vincent","orcid":null},"institutions":[{"id":"https://openalex.org/I111236770","display_name":"University of Vermont","ror":"https://ror.org/0155zta11","country_code":"US","type":"education","lineage":["https://openalex.org/I111236770"]},{"id":"https://openalex.org/I4210088533","display_name":"Vermont Oxford Network","ror":"https://ror.org/003gt3k37","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210088533"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James J Vincent","raw_affiliation_strings":["Department of Biology, University of Vermont, Burlington, VT, USA","Vermont Genetics Network Bioinformatics Core, University of Vermont, Burlington, VT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Vermont, Burlington, VT, USA","institution_ids":["https://openalex.org/I111236770"]},{"raw_affiliation_string":"Vermont Genetics Network Bioinformatics Core, University of Vermont, Burlington, VT, USA","institution_ids":["https://openalex.org/I4210088533","https://openalex.org/I111236770"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070253378","display_name":"Alicia M. Ebert","orcid":"https://orcid.org/0000-0002-1112-2009"},"institutions":[{"id":"https://openalex.org/I111236770","display_name":"University of Vermont","ror":"https://ror.org/0155zta11","country_code":"US","type":"education","lineage":["https://openalex.org/I111236770"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alicia M Ebert","raw_affiliation_strings":["Department of Biology, University of Vermont, Burlington, VT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Vermont, Burlington, VT, USA","institution_ids":["https://openalex.org/I111236770"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000554558","display_name":"Bryan A. Ballif","orcid":"https://orcid.org/0000-0001-7650-3817"},"institutions":[{"id":"https://openalex.org/I111236770","display_name":"University of Vermont","ror":"https://ror.org/0155zta11","country_code":"US","type":"education","lineage":["https://openalex.org/I111236770"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Bryan A Ballif","raw_affiliation_strings":["Department of Biology, University of Vermont, Burlington, VT, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Vermont, Burlington, VT, USA","institution_ids":["https://openalex.org/I111236770"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5000554558"],"corresponding_institution_ids":["https://openalex.org/I111236770"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1862,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.5309563,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"34","issue":"22","first_page":"3898","last_page":"3906"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13157","display_name":"Cancer-related gene regulation","score":1.0,"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/T13157","display_name":"Cancer-related gene regulation","score":1.0,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.998199999332428,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9901000261306763,"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/adapter-molecule-crk","display_name":"Adapter molecule crk","score":0.9196264743804932},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.7162992358207703},{"id":"https://openalex.org/keywords/signal-transducing-adaptor-protein","display_name":"Signal transducing adaptor protein","score":0.6214408278465271},{"id":"https://openalex.org/keywords/sh2-domain","display_name":"SH2 domain","score":0.607237696647644},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5849224328994751},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.553614616394043},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5488317012786865},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4633724093437195},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.4401308298110962},{"id":"https://openalex.org/keywords/phosphorylation","display_name":"Phosphorylation","score":0.3276544213294983},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.2305763065814972},{"id":"https://openalex.org/keywords/proto-oncogene-tyrosine-protein-kinase-src","display_name":"Proto-oncogene tyrosine-protein kinase Src","score":0.22042390704154968},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2090768814086914},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07465434074401855}],"concepts":[{"id":"https://openalex.org/C133570447","wikidata":"https://www.wikidata.org/wiki/Q17909794","display_name":"Adapter molecule crk","level":4,"score":0.9196264743804932},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7162992358207703},{"id":"https://openalex.org/C183786373","wikidata":"https://www.wikidata.org/wiki/Q5964993","display_name":"Signal transducing adaptor protein","level":3,"score":0.6214408278465271},{"id":"https://openalex.org/C197153747","wikidata":"https://www.wikidata.org/wiki/Q24780316","display_name":"SH2 domain","level":4,"score":0.607237696647644},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5849224328994751},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.553614616394043},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5488317012786865},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4633724093437195},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.4401308298110962},{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.3276544213294983},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.2305763065814972},{"id":"https://openalex.org/C108636557","wikidata":"https://www.wikidata.org/wiki/Q21109354","display_name":"Proto-oncogene tyrosine-protein kinase Src","level":3,"score":0.22042390704154968},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2090768814086914},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07465434074401855},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018909","descriptor_name":"src Homology Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018909","descriptor_name":"src Homology Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018909","descriptor_name":"src Homology Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D048868","descriptor_name":"Adaptor Proteins, Signal Transducing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048868","descriptor_name":"Adaptor Proteins, Signal Transducing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048868","descriptor_name":"Adaptor Proteins, Signal Transducing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty434","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty434","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/22/3898/26441449/bty434.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:29868839","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29868839","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:pubmedcentral.nih.gov:6223376","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6223376","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty434","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty434","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/22/3898/26441449/bty434.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":[],"awards":[{"id":"https://openalex.org/G1799731340","display_name":null,"funder_award_id":"1656510","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2007488712","display_name":null,"funder_award_id":"8P20GM103449","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5625968729","display_name":null,"funder_award_id":"5P20RR016435","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G651165682","display_name":null,"funder_award_id":"1021795","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2806774184.pdf","grobid_xml":"https://content.openalex.org/works/W2806774184.grobid-xml"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W158709665","https://openalex.org/W1757809043","https://openalex.org/W1977560411","https://openalex.org/W1978550291","https://openalex.org/W1979051854","https://openalex.org/W1987279602","https://openalex.org/W1988805210","https://openalex.org/W1990848928","https://openalex.org/W1999916818","https://openalex.org/W2001152066","https://openalex.org/W2015619702","https://openalex.org/W2016850259","https://openalex.org/W2019564264","https://openalex.org/W2019592149","https://openalex.org/W2050067448","https://openalex.org/W2057616220","https://openalex.org/W2060791849","https://openalex.org/W2070983416","https://openalex.org/W2070996331","https://openalex.org/W2072021181","https://openalex.org/W2089375674","https://openalex.org/W2093573061","https://openalex.org/W2096967258","https://openalex.org/W2101876702","https://openalex.org/W2110578000","https://openalex.org/W2126254010","https://openalex.org/W2139429540","https://openalex.org/W2146926661","https://openalex.org/W2148066913","https://openalex.org/W2152396103","https://openalex.org/W2159220993","https://openalex.org/W2159452410","https://openalex.org/W2164053775","https://openalex.org/W2166645045","https://openalex.org/W2168401498","https://openalex.org/W2168724722","https://openalex.org/W2189707966","https://openalex.org/W2263371256","https://openalex.org/W2316064308","https://openalex.org/W2326722293","https://openalex.org/W2330212158","https://openalex.org/W2407247987","https://openalex.org/W2559482520","https://openalex.org/W2570732803","https://openalex.org/W2611624100","https://openalex.org/W2747148721","https://openalex.org/W2762033819","https://openalex.org/W4239954108","https://openalex.org/W4250134843","https://openalex.org/W6637701581","https://openalex.org/W6821648423"],"related_works":["https://openalex.org/W2134567861","https://openalex.org/W4313391696","https://openalex.org/W4229706053","https://openalex.org/W2172394564","https://openalex.org/W2436536428","https://openalex.org/W2057603067","https://openalex.org/W2409756128","https://openalex.org/W2074198937","https://openalex.org/W1985057592","https://openalex.org/W2013452351"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2019,"cited_by_count":2}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2018-06-13T00:00:00"}