{"id":"https://openalex.org/W4403298794","doi":"https://doi.org/10.1093/bioinformatics/btae602","title":"Sitetack: a deep learning model that improves PTM prediction by using known PTMs","display_name":"Sitetack: a deep learning model that improves PTM prediction by using known PTMs","publication_year":2024,"publication_date":"2024-10-08","ids":{"openalex":"https://openalex.org/W4403298794","doi":"https://doi.org/10.1093/bioinformatics/btae602","pmid":"https://pubmed.ncbi.nlm.nih.gov/39388212"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae602","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae602","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae602/59713762/btae602.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae602/59713762/btae602.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057259263","display_name":"Clair S. Gutierrez","orcid":"https://orcid.org/0000-0001-9235-7223"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Clair S Gutierrez","raw_affiliation_strings":["Broad Institute of MIT and Harvard , Cambridge, MA 02143,","Department of Chemistry, Massachusetts Institute of Technology , Cambridge, MA 02139,","Broad Institute of MIT and Harvard, Cambridge, MA United States","Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States"],"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA 02143,","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Chemistry, Massachusetts Institute of Technology , Cambridge, MA 02139,","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA United States","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104320146","display_name":"Alia A. Kassim","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alia A Kassim","raw_affiliation_strings":["Department of Chemistry, Massachusetts Institute of Technology , Cambridge, MA 02139,","Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Massachusetts Institute of Technology , Cambridge, MA 02139,","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102682092","display_name":"Benjamin D. Gutierrez","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Benjamin D Gutierrez","raw_affiliation_strings":["Independent Researcher"],"affiliations":[{"raw_affiliation_string":"Independent Researcher","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019213891","display_name":"Ronald T. Raines","orcid":"https://orcid.org/0000-0001-7164-1719"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I4390039253","display_name":"Koch Institute for Integrative Cancer Research At MIT","ror":"https://ror.org/01xd6q208","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4390039253","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ronald T Raines","raw_affiliation_strings":["Broad Institute of MIT and Harvard , Cambridge, MA 02143,","Department of Chemistry, Massachusetts Institute of Technology , Cambridge, MA 02139,","Koch Institute for Integrated Cancer Research at MIT , Cambridge, MA 02139,","Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States","Koch Institute for Integrated Cancer Research at MIT, Cambridge, MA United States","Broad Institute of MIT and Harvard, Cambridge, MA United States"],"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard , Cambridge, MA 02143,","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Chemistry, Massachusetts Institute of Technology , Cambridge, MA 02139,","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Koch Institute for Integrated Cancer Research at MIT , Cambridge, MA 02139,","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Koch Institute for Integrated Cancer Research at MIT, Cambridge, MA United States","institution_ids":["https://openalex.org/I4390039253"]},{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA United States","institution_ids":["https://openalex.org/I107606265"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5057259263"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I63966007"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.8804,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.91258716,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"40","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11326","display_name":"Stock Market Forecasting Methods","score":0.1234000027179718,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11326","display_name":"Stock Market Forecasting Methods","score":0.1234000027179718,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.656145453453064},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.49948906898498535},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.49601659178733826},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4042378067970276}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.656145453453064},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.49948906898498535},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49601659178733826},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4042378067970276}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae602","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae602","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae602/59713762/btae602.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39388212","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39388212","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:11552626","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11552626","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11552626/pdf/btae602.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae602","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae602","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae602/59713762/btae602.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5695224068","display_name":null,"funder_award_id":"R35 GM148220","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6149902136","display_name":null,"funder_award_id":"R01 CA073808","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8926491534","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320333566","funder_display_name":"National Defense Science and Engineering Graduate"}],"funders":[{"id":"https://openalex.org/F4320309369","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320333566","display_name":"National Defense Science and Engineering Graduate","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403298794.pdf","grobid_xml":"https://content.openalex.org/works/W4403298794.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1981149222","https://openalex.org/W2001326517","https://openalex.org/W2028161249","https://openalex.org/W2038113278","https://openalex.org/W2140409722","https://openalex.org/W2150593711","https://openalex.org/W2156125289","https://openalex.org/W2158266834","https://openalex.org/W2161162374","https://openalex.org/W2170747616","https://openalex.org/W2187089797","https://openalex.org/W2476542314","https://openalex.org/W2742750032","https://openalex.org/W2768826694","https://openalex.org/W2802147764","https://openalex.org/W2897702642","https://openalex.org/W2903682118","https://openalex.org/W2906946803","https://openalex.org/W2920338801","https://openalex.org/W2963950918","https://openalex.org/W2971922425","https://openalex.org/W2984076969","https://openalex.org/W3015502856","https://openalex.org/W3020440546","https://openalex.org/W3094498635","https://openalex.org/W3119372191","https://openalex.org/W3127515140","https://openalex.org/W3152110994","https://openalex.org/W3161574662","https://openalex.org/W3185245858","https://openalex.org/W3216341395","https://openalex.org/W4205886009","https://openalex.org/W4223515782","https://openalex.org/W4281730031","https://openalex.org/W4287881765","https://openalex.org/W4309506674","https://openalex.org/W4315642941","https://openalex.org/W4322208336","https://openalex.org/W4361001942","https://openalex.org/W4366083739","https://openalex.org/W4384283453","https://openalex.org/W4389385479"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W2961085424","https://openalex.org/W3215138031","https://openalex.org/W4306674287","https://openalex.org/W3009238340","https://openalex.org/W4321369474","https://openalex.org/W4360585206","https://openalex.org/W4285208911","https://openalex.org/W3046775127","https://openalex.org/W3082895349"],"abstract_inverted_index":{"Sitetack":[0],"is":[1],"available":[2,22],"as":[3],"a":[4],"web":[5],"tool":[6],"at":[7,23],"https://sitetack.net;":[8],"the":[9],"source":[10],"code,":[11],"representative":[12],"datasets,":[13],"instructions":[14],"for":[15],"local":[16],"use,":[17],"and":[18],"select":[19],"models":[20],"are":[21],"https://github.com/clair-gutierrez/sitetack.":[24]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
