{"id":"https://openalex.org/W4295765292","doi":"https://doi.org/10.3390/axioms11090469","title":"PTG-PLM: Predicting Post-Translational Glycosylation and Glycation Sites Using Protein Language Models and Deep Learning","display_name":"PTG-PLM: Predicting Post-Translational Glycosylation and Glycation Sites Using Protein Language Models and Deep Learning","publication_year":2022,"publication_date":"2022-09-14","ids":{"openalex":"https://openalex.org/W4295765292","doi":"https://doi.org/10.3390/axioms11090469"},"language":"en","primary_location":{"id":"doi:10.3390/axioms11090469","is_oa":true,"landing_page_url":"https://doi.org/10.3390/axioms11090469","pdf_url":"https://www.mdpi.com/2075-1680/11/9/469/pdf?version=1663129409","source":{"id":"https://openalex.org/S4210173132","display_name":"Axioms","issn_l":"2075-1680","issn":["2075-1680"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Axioms","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2075-1680/11/9/469/pdf?version=1663129409","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005657807","display_name":"Alhasan Alkuhlani","orcid":"https://orcid.org/0000-0003-0725-9923"},"institutions":[{"id":"https://openalex.org/I107720978","display_name":"Ain Shams University","ror":"https://ror.org/00cb9w016","country_code":"EG","type":"education","lineage":["https://openalex.org/I107720978"]},{"id":"https://openalex.org/I170535673","display_name":"Sana'a University","ror":"https://ror.org/04hcvaf32","country_code":"YE","type":"education","lineage":["https://openalex.org/I170535673"]}],"countries":["EG","YE"],"is_corresponding":false,"raw_author_name":"Alhasan Alkuhlani","raw_affiliation_strings":["Faculty of Computer and Information Science, Ain Shams University, Cairo 11566, Egypt","Faculty of Computer and Information Technology, Sana\u2019a University, Sana\u2019a 1247, Yemen","Faculty of Computer and Information Technology, Sana'a University, Sana'a 1247, Yemen"],"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, Ain Shams University, Cairo 11566, Egypt","institution_ids":["https://openalex.org/I107720978"]},{"raw_affiliation_string":"Faculty of Computer and Information Technology, Sana\u2019a University, Sana\u2019a 1247, Yemen","institution_ids":["https://openalex.org/I170535673"]},{"raw_affiliation_string":"Faculty of Computer and Information Technology, Sana'a University, Sana'a 1247, Yemen","institution_ids":["https://openalex.org/I170535673"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033458445","display_name":"Walaa Gad","orcid":"https://orcid.org/0000-0002-7816-3518"},"institutions":[{"id":"https://openalex.org/I107720978","display_name":"Ain Shams University","ror":"https://ror.org/00cb9w016","country_code":"EG","type":"education","lineage":["https://openalex.org/I107720978"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Walaa Gad","raw_affiliation_strings":["Faculty of Computer and Information Science, Ain Shams University, Cairo 11566, Egypt"],"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, Ain Shams University, Cairo 11566, Egypt","institution_ids":["https://openalex.org/I107720978"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034587442","display_name":"Mohamed Roushdy","orcid":"https://orcid.org/0000-0002-9655-3229"},"institutions":[{"id":"https://openalex.org/I186217134","display_name":"Future University in Egypt","ror":"https://ror.org/03s8c2x09","country_code":"EG","type":"education","lineage":["https://openalex.org/I186217134"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Mohamed Roushdy","raw_affiliation_strings":["Faculty of Computers and Information Technology, Future University in Egypt, New Cairo 11835, Egypt"],"affiliations":[{"raw_affiliation_string":"Faculty of Computers and Information Technology, Future University in Egypt, New Cairo 11835, Egypt","institution_ids":["https://openalex.org/I186217134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020485335","display_name":"Michael Gr. Voskoglou","orcid":"https://orcid.org/0000-0002-4727-0089"},"institutions":[{"id":"https://openalex.org/I1319660883","display_name":"Technological Educational Institute of Western Greece","ror":"https://ror.org/01mymm084","country_code":"GR","type":"education","lineage":["https://openalex.org/I1319660883"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Michael Gr. Voskoglou","raw_affiliation_strings":["Department of Applied Mathematics, Graduate Technological Educational Institute of Western Greece, 22334 Patras, Greece"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, Graduate Technological Educational Institute of Western Greece, 22334 Patras, Greece","institution_ids":["https://openalex.org/I1319660883"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061699800","display_name":"Abdel-Badeeh M. Salem","orcid":"https://orcid.org/0000-0001-5013-4339"},"institutions":[{"id":"https://openalex.org/I107720978","display_name":"Ain Shams University","ror":"https://ror.org/00cb9w016","country_code":"EG","type":"education","lineage":["https://openalex.org/I107720978"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Abdel-badeeh M. Salem","raw_affiliation_strings":["Faculty of Computer and Information Science, Ain Shams University, Cairo 11566, Egypt"],"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Science, Ain Shams University, Cairo 11566, Egypt","institution_ids":["https://openalex.org/I107720978"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5020485335"],"corresponding_institution_ids":["https://openalex.org/I1319660883"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":1.8871,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.86312053,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"11","issue":"9","first_page":"469","last_page":"469"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9995999932289124,"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":0.9995999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9821000099182129,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9627000093460083,"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/glycosylation","display_name":"Glycosylation","score":0.7704944610595703},{"id":"https://openalex.org/keywords/glycation","display_name":"Glycation","score":0.7265961170196533},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5261873006820679},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.44076332449913025},{"id":"https://openalex.org/keywords/posttranslational-modification","display_name":"Posttranslational modification","score":0.42644333839416504},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4217678904533386},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.33943426609039307},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1995377540588379},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1769799292087555}],"concepts":[{"id":"https://openalex.org/C2777313579","wikidata":"https://www.wikidata.org/wiki/Q898365","display_name":"Glycosylation","level":2,"score":0.7704944610595703},{"id":"https://openalex.org/C147990577","wikidata":"https://www.wikidata.org/wiki/Q25790","display_name":"Glycation","level":3,"score":0.7265961170196533},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5261873006820679},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44076332449913025},{"id":"https://openalex.org/C100631289","wikidata":"https://www.wikidata.org/wiki/Q898362","display_name":"Posttranslational modification","level":3,"score":0.42644333839416504},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4217678904533386},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33943426609039307},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1995377540588379},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1769799292087555},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3390/axioms11090469","is_oa":true,"landing_page_url":"https://doi.org/10.3390/axioms11090469","pdf_url":"https://www.mdpi.com/2075-1680/11/9/469/pdf?version=1663129409","source":{"id":"https://openalex.org/S4210173132","display_name":"Axioms","issn_l":"2075-1680","issn":["2075-1680"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Axioms","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:35a3fc0fae9248fd845d11670c6e64f7","is_oa":true,"landing_page_url":"https://doaj.org/article/35a3fc0fae9248fd845d11670c6e64f7","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Axioms, Vol 11, Iss 9, p 469 (2022)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2075-1680/11/9/469/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/axioms11090469","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Axioms; Volume 11; Issue 9; Pages: 469","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/axioms11090469","is_oa":true,"landing_page_url":"https://doi.org/10.3390/axioms11090469","pdf_url":"https://www.mdpi.com/2075-1680/11/9/469/pdf?version=1663129409","source":{"id":"https://openalex.org/S4210173132","display_name":"Axioms","issn_l":"2075-1680","issn":["2075-1680"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Axioms","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4295765292.pdf","grobid_xml":"https://content.openalex.org/works/W4295765292.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W2014509414","https://openalex.org/W2050566492","https://openalex.org/W2076746539","https://openalex.org/W2088456241","https://openalex.org/W2101234009","https://openalex.org/W2102461176","https://openalex.org/W2103525038","https://openalex.org/W2112796928","https://openalex.org/W2131774270","https://openalex.org/W2147526198","https://openalex.org/W2153456067","https://openalex.org/W2170747616","https://openalex.org/W2295598076","https://openalex.org/W2492513888","https://openalex.org/W2528774686","https://openalex.org/W2555891876","https://openalex.org/W2739999456","https://openalex.org/W2742750032","https://openalex.org/W2764095180","https://openalex.org/W2765093153","https://openalex.org/W2801931817","https://openalex.org/W2810819381","https://openalex.org/W2905744876","https://openalex.org/W2906946803","https://openalex.org/W2911904997","https://openalex.org/W2911964244","https://openalex.org/W2921654911","https://openalex.org/W2922210059","https://openalex.org/W2939599083","https://openalex.org/W2950813464","https://openalex.org/W2951433247","https://openalex.org/W2953008890","https://openalex.org/W2971851828","https://openalex.org/W2979040066","https://openalex.org/W2984076969","https://openalex.org/W3014321973","https://openalex.org/W3032445823","https://openalex.org/W3035772797","https://openalex.org/W3040739508","https://openalex.org/W3084256198","https://openalex.org/W3093596417","https://openalex.org/W3100777112","https://openalex.org/W3120137197","https://openalex.org/W3144701084","https://openalex.org/W3146944767","https://openalex.org/W3156754474","https://openalex.org/W3159343835","https://openalex.org/W3166142427","https://openalex.org/W3172422681","https://openalex.org/W3184367114","https://openalex.org/W3195222011","https://openalex.org/W3216325381","https://openalex.org/W4210427888","https://openalex.org/W4210608406","https://openalex.org/W4212994316","https://openalex.org/W4225438928","https://openalex.org/W4226190967","https://openalex.org/W4239510810","https://openalex.org/W6663129799","https://openalex.org/W6675354045","https://openalex.org/W6728150723","https://openalex.org/W6763868836","https://openalex.org/W6794997223","https://openalex.org/W6798447541"],"related_works":["https://openalex.org/W2564054537","https://openalex.org/W2093322204","https://openalex.org/W3693513","https://openalex.org/W4240713708","https://openalex.org/W2036195544","https://openalex.org/W4253750519","https://openalex.org/W1975686300","https://openalex.org/W2052655833","https://openalex.org/W4283798085","https://openalex.org/W2127236662"],"abstract_inverted_index":{"Post-translational":[0],"glycosylation":[1,37,138,177,221],"and":[2,33,38,59,82,139,151,164,170,178,190,208,222],"glycation":[3,39,140,179,223],"are":[4,23,69],"common":[5],"types":[6,245],"of":[7,136,230,242,246],"protein":[8,17,114],"post-translational":[9],"modifications":[10],"(PTMs)":[11],"in":[12,89],"which":[13],"glycan":[14],"binds":[15],"to":[16,43,53,78,238],"enzymatically":[18],"or":[19],"nonenzymatically,":[20],"respectively.":[21],"They":[22],"associated":[24],"with":[25,204],"various":[26],"diseases":[27],"such":[28],"as":[29,118],"coronavirus,":[30],"Alzheimer\u2019s,":[31],"cancer,":[32],"diabetes":[34],"diseases.":[35],"Identifying":[36],"sites":[40,56,241],"is":[41,57,144,168],"significant":[42],"understanding":[44],"their":[45,79],"biological":[46],"mechanisms.":[47],"However,":[48],"utilizing":[49],"experimental":[50],"laboratory":[51],"tools":[52,207],"identify":[54],"PTM":[55,74,137],"time-consuming":[58],"costly.":[60],"In":[61,85,123],"contrast,":[62],"computational":[63],"methods":[64,212],"based":[65,93,145,187,197],"on":[66,94,146,172,188,198],"machine":[67],"learning":[68,96,211],"becoming":[70],"increasingly":[71],"essential":[72],"for":[73,113,132,176,220],"site":[75,141,180,224],"prediction":[76],"due":[77],"higher":[80],"performance":[81,135,194,228],"lower":[83],"cost.":[84],"recent":[86,156],"years,":[87],"advances":[88],"Transformer-based":[90],"Language":[91,102,120],"Models":[92,121],"deep":[95],"have":[97],"been":[98],"transferred":[99],"from":[100,154],"Natural":[101],"Processing":[103],"(NLP)":[104],"into":[105],"the":[106,134,199,205,217,240,243],"proteomics":[107],"field":[108],"by":[109],"developing":[110],"language":[111],"models":[112,219],"sequence":[115],"representation":[116],"known":[117],"Protein":[119],"(PLMs).":[122],"this":[124],"work,":[125],"we":[126],"proposed":[127],"a":[128],"novel":[129],"method,":[130],"PTG-PLM,":[131],"improving":[133],"prediction.":[142,181,225],"PTG-PLM":[143,186,196,215,231],"convolutional":[147],"neural":[148],"networks":[149],"(CNNs)":[150],"embedding":[152],"extracted":[153],"six":[155],"PLMs":[157],"including":[158],"ProtBert-BFD,":[159],"ProtBert,":[160],"ProtAlbert,":[161],"ProtXlnet,":[162],"ESM-1b,":[163],"TAPE.":[165],"The":[166,182,226],"model":[167],"trained":[169],"evaluated":[171],"two":[173],"public":[174],"datasets":[175],"results":[183,203,229],"show":[184,213],"that":[185,214,233],"ESM-1b":[189],"ProtBert-BFD":[191],"has":[192],"better":[193],"than":[195],"other":[200,218,244],"PLMs.":[201],"Comparison":[202],"existing":[206],"representative":[209],"supervised":[210],"surpasses":[216],"outstanding":[227],"indicate":[232],"it":[234],"can":[235],"be":[236],"used":[237],"predict":[239],"PTMs.":[247]},"counts_by_year":[{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2022-09-15T00:00:00"}
