{"id":"https://openalex.org/W4391075295","doi":"https://doi.org/10.1093/bioinformatics/btae033","title":"Using explainable machine learning to uncover the kinase\u2013substrate interaction landscape","display_name":"Using explainable machine learning to uncover the kinase\u2013substrate interaction landscape","publication_year":2024,"publication_date":"2024-01-19","ids":{"openalex":"https://openalex.org/W4391075295","doi":"https://doi.org/10.1093/bioinformatics/btae033","pmid":"https://pubmed.ncbi.nlm.nih.gov/38244571"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae033","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae033","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae033/56284976/btae033.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/btae033/56284976/btae033.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050749778","display_name":"Zhongliang Zhou","orcid":"https://orcid.org/0000-0003-4471-6759"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhongliang Zhou","raw_affiliation_strings":["School of Computing, University of Georgia , Athens, GA 30602, United States"],"raw_orcid":"https://orcid.org/0000-0003-4471-6759","affiliations":[{"raw_affiliation_string":"School of Computing, University of Georgia , Athens, GA 30602, United States","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066141945","display_name":"Wayland Yeung","orcid":"https://orcid.org/0000-0002-2523-4984"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wayland Yeung","raw_affiliation_strings":["Institute of Bioinformatics, University of Georgia , Athens, GA 30602, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics, University of Georgia , Athens, GA 30602, United States","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036193269","display_name":"Saber Soleymani","orcid":"https://orcid.org/0000-0002-0771-4319"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Saber Soleymani","raw_affiliation_strings":["School of Computing, University of Georgia , Athens, GA 30602, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, University of Georgia , Athens, GA 30602, United States","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078827216","display_name":"Nathan Gravel","orcid":"https://orcid.org/0000-0002-8482-4255"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan Gravel","raw_affiliation_strings":["Institute of Bioinformatics, University of Georgia , Athens, GA 30602, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics, University of Georgia , Athens, GA 30602, United States","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020459889","display_name":"Mariah Salcedo","orcid":"https://orcid.org/0009-0008-0490-2446"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mariah Salcedo","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Georgia , Athens, GA 30602, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Georgia , Athens, GA 30602, United States","institution_ids":["https://openalex.org/I165733156"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100359839","display_name":"Sheng Li","orcid":"https://orcid.org/0000-0003-1205-8632"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sheng Li","raw_affiliation_strings":["School of Data Science, University of Virginia , Charlottesville, VA 22903, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Data Science, University of Virginia , Charlottesville, VA 22903, United States","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033384464","display_name":"Natarajan Kannan","orcid":"https://orcid.org/0000-0002-2833-8375"},"institutions":[{"id":"https://openalex.org/I165733156","display_name":"University of Georgia","ror":"https://ror.org/00te3t702","country_code":"US","type":"education","lineage":["https://openalex.org/I165733156"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Natarajan Kannan","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, University of Georgia , Athens, GA 30602, United States","Institute of Bioinformatics, University of Georgia , Athens, GA 30602, United States"],"raw_orcid":"https://orcid.org/0000-0002-2833-8375","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Georgia , Athens, GA 30602, United States","institution_ids":["https://openalex.org/I165733156"]},{"raw_affiliation_string":"Institute of Bioinformatics, University of Georgia , Athens, GA 30602, United States","institution_ids":["https://openalex.org/I165733156"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5033384464","https://openalex.org/A5100359839"],"corresponding_institution_ids":["https://openalex.org/I165733156","https://openalex.org/I51556381"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.8023,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.90689336,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"40","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.2865999937057495,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.2865999937057495,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.23659999668598175,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.1657000035047531,"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/kinase","display_name":"Kinase","score":0.6234362125396729},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5632364749908447},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49823689460754395},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4942910671234131},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.48957356810569763},{"id":"https://openalex.org/keywords/protein-kinase-a","display_name":"Protein kinase A","score":0.4203416705131531},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.413273423910141},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3817276656627655},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3539782464504242},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.340958833694458},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.31339433789253235},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.17641735076904297},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.10301074385643005}],"concepts":[{"id":"https://openalex.org/C184235292","wikidata":"https://www.wikidata.org/wiki/Q421851","display_name":"Kinase","level":2,"score":0.6234362125396729},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5632364749908447},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49823689460754395},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4942910671234131},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.48957356810569763},{"id":"https://openalex.org/C97029542","wikidata":"https://www.wikidata.org/wiki/Q281417","display_name":"Protein kinase A","level":3,"score":0.4203416705131531},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.413273423910141},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3817276656627655},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3539782464504242},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.340958833694458},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.31339433789253235},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.17641735076904297},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.10301074385643005}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":"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":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019151","descriptor_name":"Peptide Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae033","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae033","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae033/56284976/btae033.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:38244571","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38244571","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:10868336","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10868336","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10868336/pdf/btae033.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae033","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae033","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae033/56284976/btae033.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/G1339835966","display_name":null,"funder_award_id":"R01 HS029009","funder_id":"https://openalex.org/F4320332177","funder_display_name":"Agency for Healthcare Research and Quality"},{"id":"https://openalex.org/G3609227936","display_name":null,"funder_award_id":"R35GM139656","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4901234936","display_name":null,"funder_award_id":"R35 GM139656","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6718309948","display_name":null,"funder_award_id":"R01HS029009","funder_id":"https://openalex.org/F4320332177","funder_display_name":"Agency for Healthcare Research and Quality"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332177","display_name":"Agency for Healthcare Research and Quality","ror":"https://ror.org/03jmfdf59"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391075295.pdf"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1875580551","https://openalex.org/W1970566610","https://openalex.org/W2030205108","https://openalex.org/W2129888542","https://openalex.org/W2157658519","https://openalex.org/W2170678561","https://openalex.org/W2742750032","https://openalex.org/W2906946803","https://openalex.org/W2954422262","https://openalex.org/W2962862931","https://openalex.org/W3146944767","https://openalex.org/W3185245858","https://openalex.org/W4210871270","https://openalex.org/W4295216797","https://openalex.org/W4315642941","https://openalex.org/W4317868880","https://openalex.org/W6737947904"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W4390569940","https://openalex.org/W4361193272","https://openalex.org/W2963326959","https://openalex.org/W4388685194","https://openalex.org/W4312407344","https://openalex.org/W2894289927"],"abstract_inverted_index":{"MOTIVATION:":[0],"Phosphorylation,":[1],"a":[2,34,48,67,165,197,208],"post-translational":[3],"modification":[4],"regulated":[5],"by":[6],"protein":[7,27],"kinase":[8,177],"enzymes,":[9],"plays":[10],"an":[11,92],"essential":[12],"role":[13],"in":[14,37,133,190],"almost":[15],"all":[16],"cellular":[17],"processes.":[18],"Understanding":[19],"how":[20],"each":[21],"of":[22,69,86,152,168],"the":[23,117,146,162,191,212],"nearly":[24],"500":[25],"human":[26],"kinases":[28,89,130],"selectively":[29],"phosphorylates":[30],"their":[31],"substrates":[32],"is":[33,229],"foundational":[35],"challenge":[36],"bioinformatics":[38],"and":[39,60,176,207,221],"cell":[40],"signaling.":[41],"Although":[42],"deep":[43],"learning":[44,113,142],"models":[45,56],"have":[46],"been":[47],"popular":[49],"means":[50],"to":[51,81,90,144],"predict":[52],"kinase-substrate":[53,202,214],"relationships,":[54],"existing":[55],"often":[57],"lack":[58],"interpretability":[59],"are":[61,223],"trained":[62,102],"on":[63,104,121,128],"datasets":[64,79],"skewed":[65],"toward":[66],"subset":[68],"well-studied":[70],"kinases.":[71],"RESULTS:":[72],"Here":[73],"we":[74,138,159,195],"leverage":[75],"recent":[76],"peptide":[77,134,192],"library":[78,135],"generated":[80],"determine":[82],"substrate":[83,169,173],"specificity":[84,187],"profiles":[85],"300":[87],"serine/threonine":[88],"develop":[91],"explainable":[93,140],"Transformer":[94],"model":[95,118,163],"for":[96,200,204,210],"kinase-peptide":[97,124],"interaction":[98],"prediction.":[99],"The":[100],"model,":[101],"solely":[103],"primary":[105],"sequences,":[106],"achieved":[107],"state-of-the-art":[108],"performance.":[109],"Its":[110],"unique":[111,166],"multitask":[112],"paradigm":[114],"built":[115],"within":[116],"enables":[119],"predictions":[120,127],"virtually":[122],"any":[123],"pair,":[125],"including":[126],"139":[129],"not":[131],"used":[132],"screens.":[136],"Furthermore,":[137],"employed":[139],"machine":[141],"methods":[143],"elucidate":[145],"model's":[147],"inner":[148],"workings.":[149],"Through":[150],"analysis":[151,184],"learned":[153,213],"embeddings":[154],"at":[155,225,231],"different":[156],"training":[157],"stages,":[158],"demonstrate":[160],"that":[161],"employs":[164],"strategy":[167],"prediction":[170],"considering":[171],"both":[172],"motif":[174],"patterns":[175],"evolutionary":[178],"features.":[179],"SHapley":[180],"Additive":[181],"exPlanation":[182],"(SHAP)":[183],"reveals":[185],"key":[186],"determining":[188],"residues":[189],"sequence.":[193],"Finally,":[194],"provide":[196],"web":[198],"interface":[199],"predicting":[201],"associations":[203],"user-defined":[205],"sequences":[206],"resource":[209],"visualizing":[211],"associations.":[215],"AVAILABILITY":[216],"AND":[217],"IMPLEMENTATION:":[218],"All":[219],"code":[220],"data":[222],"available":[224,230],"https://github.com/esbgkannan/Phosformer-ST.":[226],"Web":[227],"server":[228],"https://phosformer.netlify.app.":[232]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-11T18:08:03.149640","created_date":"2025-10-10T00:00:00"}
