{"id":"https://openalex.org/W4395118066","doi":"https://doi.org/10.1093/bioinformatics/btae290","title":"LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model","display_name":"LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model","publication_year":2024,"publication_date":"2024-04-25","ids":{"openalex":"https://openalex.org/W4395118066","doi":"https://doi.org/10.1093/bioinformatics/btae290","pmid":"https://pubmed.ncbi.nlm.nih.gov/38662579"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae290","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae290","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae290/57334068/btae290.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/btae290/57334068/btae290.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042796326","display_name":"Pawel Pratyush","orcid":"https://orcid.org/0000-0002-4210-1200"},"institutions":[{"id":"https://openalex.org/I11957088","display_name":"Michigan Technological University","ror":"https://ror.org/0036rpn28","country_code":"US","type":"education","lineage":["https://openalex.org/I11957088"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pawel Pratyush","raw_affiliation_strings":["Department of Computer Science, Michigan Technological University , Houghton, MI 49931, United States","Department of Computer Science, Michigan Technological University, Houghton, 49931, Michigan, United States"],"raw_orcid":"https://orcid.org/0000-0002-4210-1200","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Michigan Technological University , Houghton, MI 49931, United States","institution_ids":["https://openalex.org/I11957088"]},{"raw_affiliation_string":"Department of Computer Science, Michigan Technological University, Houghton, 49931, Michigan, United States","institution_ids":["https://openalex.org/I11957088","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048933274","display_name":"Soufia Bahmani","orcid":"https://orcid.org/0000-0001-8266-6700"},"institutions":[{"id":"https://openalex.org/I11957088","display_name":"Michigan Technological University","ror":"https://ror.org/0036rpn28","country_code":"US","type":"education","lineage":["https://openalex.org/I11957088"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Soufia Bahmani","raw_affiliation_strings":["Department of Computer Science, Michigan Technological University , Houghton, MI 49931, United States","Department of Computer Science, Michigan Technological University, Houghton, 49931, Michigan, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Michigan Technological University , Houghton, MI 49931, United States","institution_ids":["https://openalex.org/I11957088"]},{"raw_affiliation_string":"Department of Computer Science, Michigan Technological University, Houghton, 49931, Michigan, United States","institution_ids":["https://openalex.org/I11957088","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052273419","display_name":"Suresh Pokharel","orcid":"https://orcid.org/0000-0003-1495-2953"},"institutions":[{"id":"https://openalex.org/I11957088","display_name":"Michigan Technological University","ror":"https://ror.org/0036rpn28","country_code":"US","type":"education","lineage":["https://openalex.org/I11957088"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suresh Pokharel","raw_affiliation_strings":["Department of Computer Science, Michigan Technological University , Houghton, MI 49931, United States","Department of Computer Science, Michigan Technological University, Houghton, 49931, Michigan, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Michigan Technological University , Houghton, MI 49931, United States","institution_ids":["https://openalex.org/I11957088"]},{"raw_affiliation_string":"Department of Computer Science, Michigan Technological University, Houghton, 49931, Michigan, United States","institution_ids":["https://openalex.org/I11957088","https://openalex.org/I4210111179"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083740587","display_name":"Hamid D. Ismail","orcid":"https://orcid.org/0000-0002-2690-5655"},"institutions":[{"id":"https://openalex.org/I11957088","display_name":"Michigan Technological University","ror":"https://ror.org/0036rpn28","country_code":"US","type":"education","lineage":["https://openalex.org/I11957088"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hamid D Ismail","raw_affiliation_strings":["Department of Computer Science, Michigan Technological University , Houghton, MI 49931, United States","Department of Computer Science, Michigan Technological University, Houghton, 49931, Michigan, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Michigan Technological University , Houghton, MI 49931, United States","institution_ids":["https://openalex.org/I11957088"]},{"raw_affiliation_string":"Department of Computer Science, Michigan Technological University, Houghton, 49931, Michigan, United States","institution_ids":["https://openalex.org/I11957088","https://openalex.org/I4210111179"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069061591","display_name":"Dukka B. KC","orcid":"https://orcid.org/0000-0001-7443-1928"},"institutions":[{"id":"https://openalex.org/I11957088","display_name":"Michigan Technological University","ror":"https://ror.org/0036rpn28","country_code":"US","type":"education","lineage":["https://openalex.org/I11957088"]},{"id":"https://openalex.org/I4210111179","display_name":"Michigan United","ror":"https://ror.org/0291ys696","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210111179"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dukka B KC","raw_affiliation_strings":["Department of Computer Science, Michigan Technological University , Houghton, MI 49931, United States","Department of Computer Science, Michigan Technological University, Houghton, 49931, Michigan, United States"],"raw_orcid":"https://orcid.org/0000-0001-7443-1928","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Michigan Technological University , Houghton, MI 49931, United States","institution_ids":["https://openalex.org/I11957088"]},{"raw_affiliation_string":"Department of Computer Science, Michigan Technological University, Houghton, 49931, Michigan, United States","institution_ids":["https://openalex.org/I11957088","https://openalex.org/I4210111179"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":4.0116,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.94525256,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"40","issue":"5","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":0.4260999858379364,"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":0.4260999858379364,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.1729000061750412,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.07450000196695328,"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/embedding","display_name":"Embedding","score":0.7791792750358582},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6656312942504883},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.6507657766342163},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.5482223629951477},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5340332984924316},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5298725366592407},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5250318646430969},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.45328548550605774},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.43045946955680847},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39897412061691284},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.37416476011276245},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3725767731666565},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11078011989593506}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.7791792750358582},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6656312942504883},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.6507657766342163},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.5482223629951477},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5340332984924316},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5298725366592407},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5250318646430969},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.45328548550605774},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.43045946955680847},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39897412061691284},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.37416476011276245},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3725767731666565},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11078011989593506},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"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":"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":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","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":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","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":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btae290","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae290","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae290/57334068/btae290.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:38662579","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38662579","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:11088740","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11088740","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11088740/pdf/btae290.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"},{"id":"pmh:oai:digitalcommons.mtu.edu:michigantech-p2-1726","is_oa":true,"landing_page_url":"https://digitalcommons.mtu.edu/michigantech-p2/726","pdf_url":null,"source":{"id":"https://openalex.org/S4377196391","display_name":"Digital Commons - Michigan Tech (Michigan Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I11957088","host_organization_name":"Michigan Technological University","host_organization_lineage":["https://openalex.org/I11957088"],"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":"Michigan Tech Publications","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae290","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae290","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae290/57334068/btae290.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":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.5400000214576721}],"awards":[{"id":"https://openalex.org/G5636599382","display_name":"Collaborative Research: ABI Development: Integrated platforms for protein structure and function predictions","funder_award_id":"1564606","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6824850332","display_name":null,"funder_award_id":"# 1564606","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7351746027","display_name":null,"funder_award_id":"# 1901793","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7599565429","display_name":"Excellence in Research: Deep Learning based approaches for protein post-translational modification site prediction","funder_award_id":"1901793","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/F4320311636","display_name":"Michigan Department of Health and Human Services","ror":"https://ror.org/03tpyg842"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4395118066.pdf"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W28412257","https://openalex.org/W2593128459","https://openalex.org/W2621036017","https://openalex.org/W2748860630","https://openalex.org/W3010697764","https://openalex.org/W3048991675","https://openalex.org/W3049692992","https://openalex.org/W3094567318","https://openalex.org/W3181979416","https://openalex.org/W3207838037","https://openalex.org/W4200111237","https://openalex.org/W4210810268","https://openalex.org/W4281291878","https://openalex.org/W4285160370","https://openalex.org/W4288089799","https://openalex.org/W4303645584","https://openalex.org/W4311761046","https://openalex.org/W4317369987","https://openalex.org/W4319594176","https://openalex.org/W4327550249","https://openalex.org/W4384498728","https://openalex.org/W4388422476","https://openalex.org/W4389085025","https://openalex.org/W6769627184"],"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/W2275988210"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recent":[1],"advancements":[2],"in":[3,20,126,152,236],"natural":[4],"language":[5,17],"processing":[6],"have":[7],"highlighted":[8],"the":[9,28,69,76,105,109,146,158,163,181,187,205,240],"effectiveness":[10],"of":[11,50,71,75,82,104,136,148,180,190],"global":[12],"contextualized":[13],"representations":[14],"from":[15,162,200,207],"protein":[16,63],"models":[18],"(pLMs)":[19],"numerous":[21],"downstream":[22],"tasks.":[23],"Nonetheless,":[24],"strategies":[25],"to":[26,100],"encode":[27],"site-of-interest":[29,77,106],"leveraging":[30],"pLMs":[31,54],"for":[32,52,173],"per-residue":[33,73],"prediction":[34,182],"tasks,":[35],"such":[36],"as":[37,78,80,115],"crotonylation":[38],"(Kcr)":[39],"prediction,":[40],"remain":[41],"largely":[42],"uncharted.":[43],"RESULTS:":[44],"Herein,":[45],"we":[46,92,142,185],"adopt":[47],"a":[48,94,177,232],"range":[49],"approaches":[51],"utilizing":[53,72,137],"by":[55,108,156,169,192],"experimenting":[56],"with":[57],"different":[58],"input":[59],"sequence":[60,64,222],"types":[61],"(full-length":[62],"versus":[65],"window":[66,83,221],"sequence),":[67],"assessing":[68],"implications":[70],"embedding":[74,150,209],"well":[79],"embeddings":[81,103],"residues":[84],"centered":[85],"around":[86],"it.":[87],"Building":[88],"upon":[89],"these":[90,174],"insights,":[91],"developed":[93],"novel":[95],"residual":[96],"ConvBiLSTM":[97],"network":[98],"designed":[99],"process":[101],"window-level":[102,140],"generated":[107],"ProtT5-XL-UniRef50":[110],"pLM":[111],"using":[112,218],"full-length":[113],"sequences":[114],"input.":[116],"This":[117],"model,":[118,228],"termed":[119],"T5ResConvBiLSTM,":[120],"surpasses":[121],"existing":[122],"state-of-the-art":[123],"Kcr":[124],"predictors":[125],"performance":[127,238],"across":[128,239],"three":[129],"diverse":[130],"datasets.":[131,242],"To":[132],"validate":[133],"our":[134],"approach":[135],"full":[138],"sequence-based":[139],"embeddings,":[141],"also":[143],"delved":[144],"into":[145],"interpretability":[147],"ProtT5-derived":[149],"tensors":[151],"two":[153,194],"ways:":[154],"firstly,":[155],"scrutinizing":[157],"attention":[159],"weights":[160],"obtained":[161],"transformer's":[164],"encoder":[165],"block;":[166],"and":[167,204],"secondly,":[168],"computing":[170],"SHAP":[171],"values":[172],"tensors,":[175],"providing":[176],"model-agnostic":[178],"interpretation":[179],"results.":[183],"Additionally,":[184],"enhance":[186],"latent":[188],"representation":[189],"ProtT5":[191],"incorporating":[193],"additional":[195],"local":[196],"representations,":[197],"one":[198],"derived":[199],"amino":[201],"acid":[202],"properties":[203],"other":[206],"supervised":[208],"layer,":[210],"through":[211],"an":[212,219],"intermediate":[213],"fusion":[214],"stacked":[215,227],"generalization":[216],"approach,":[217],"n-mer":[220],"(or,":[223],"peptide/fragment).":[224],"The":[225],"resultant":[226],"dubbed":[229],"LMCrot,":[230],"exhibits":[231],"more":[233],"pronounced":[234],"improvement":[235],"predictive":[237],"tested":[241],"AVAILABILITY":[243],"AND":[244],"IMPLEMENTATION:":[245],"LMCrot":[246],"is":[247],"publicly":[248],"available":[249],"at":[250],"https://github.com/KCLabMTU/LMCrot.":[251]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":6}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
