{"id":"https://openalex.org/W4416596520","doi":"https://doi.org/10.3390/info16121023","title":"Role of Machine and Deep Learning in Predicting Protein Modification Sites: Review and Future Directions","display_name":"Role of Machine and Deep Learning in Predicting Protein Modification Sites: Review and Future Directions","publication_year":2025,"publication_date":"2025-11-24","ids":{"openalex":"https://openalex.org/W4416596520","doi":"https://doi.org/10.3390/info16121023"},"language":"en","primary_location":{"id":"doi:10.3390/info16121023","is_oa":true,"landing_page_url":"https://doi.org/10.3390/info16121023","pdf_url":"https://www.mdpi.com/2078-2489/16/12/1023/pdf?version=1763980886","source":{"id":"https://openalex.org/S4210219776","display_name":"Information","issn_l":"2078-2489","issn":["2078-2489"],"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":"Information","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2078-2489/16/12/1023/pdf?version=1763980886","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Siliang Gong","orcid":"https://orcid.org/0009-0009-8386-5432"},"institutions":[{"id":"https://openalex.org/I4210115515","display_name":"Nanyang Institute of Technology","ror":"https://ror.org/0203c2755","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210115515"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Siliang Gong","raw_affiliation_strings":["School of Computer and Software, Nanyang Institute of Technology, Nanyang 473000, China"],"raw_orcid":"https://orcid.org/0009-0009-8386-5432","affiliations":[{"raw_affiliation_string":"School of Computer and Software, Nanyang Institute of Technology, Nanyang 473000, China","institution_ids":["https://openalex.org/I4210115515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078782345","display_name":"Kaiyang Qu","orcid":"https://orcid.org/0000-0001-6564-6601"},"institutions":[{"id":"https://openalex.org/I4210115515","display_name":"Nanyang Institute of Technology","ror":"https://ror.org/0203c2755","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210115515"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kaiyang Qu","raw_affiliation_strings":["School of Computer and Software, Nanyang Institute of Technology, Nanyang 473000, China"],"raw_orcid":"https://orcid.org/0000-0001-6564-6601","affiliations":[{"raw_affiliation_string":"School of Computer and Software, Nanyang Institute of Technology, Nanyang 473000, China","institution_ids":["https://openalex.org/I4210115515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5078782345"],"corresponding_institution_ids":["https://openalex.org/I4210115515"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.28785896,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"16","issue":"12","first_page":"1023","last_page":"1023"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9610000252723694,"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":0.9610000252723694,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0071000000461936,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.006099999882280827,"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/deep-learning","display_name":"Deep learning","score":0.6930999755859375},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.5001999735832214},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4226999878883362},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4099999964237213},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.37470000982284546}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7265999913215637},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6930999755859375},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6191999912261963},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5712000131607056},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5001999735832214},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4226999878883362},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4099999964237213},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.37470000982284546},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.31380000710487366},{"id":"https://openalex.org/C33676613","wikidata":"https://www.wikidata.org/wiki/Q13415176","display_name":"Dimension (graph theory)","level":2,"score":0.3086000084877014},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.28200000524520874},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2721000015735626},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.2614000141620636}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3390/info16121023","is_oa":true,"landing_page_url":"https://doi.org/10.3390/info16121023","pdf_url":"https://www.mdpi.com/2078-2489/16/12/1023/pdf?version=1763980886","source":{"id":"https://openalex.org/S4210219776","display_name":"Information","issn_l":"2078-2489","issn":["2078-2489"],"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":"Information","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:c7c48734959342cca97e79bfb9790763","is_oa":true,"landing_page_url":"https://doaj.org/article/c7c48734959342cca97e79bfb9790763","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Information, Vol 16, Iss 12, p 1023 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3390/info16121023","is_oa":true,"landing_page_url":"https://doi.org/10.3390/info16121023","pdf_url":"https://www.mdpi.com/2078-2489/16/12/1023/pdf?version=1763980886","source":{"id":"https://openalex.org/S4210219776","display_name":"Information","issn_l":"2078-2489","issn":["2078-2489"],"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":"Information","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5099855721","display_name":null,"funder_award_id":"252102220039","funder_id":"https://openalex.org/F4320336593","funder_display_name":"Henan Provincial Science and Technology Research Project"},{"id":"https://openalex.org/G5647293575","display_name":null,"funder_award_id":"62502242","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320336593","display_name":"Henan Provincial Science and Technology Research Project","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416596520.pdf"},"referenced_works_count":170,"referenced_works":["https://openalex.org/W1596947964","https://openalex.org/W1655962167","https://openalex.org/W1678356000","https://openalex.org/W1973035681","https://openalex.org/W1976521702","https://openalex.org/W1982267716","https://openalex.org/W1989064680","https://openalex.org/W1993666136","https://openalex.org/W1994807229","https://openalex.org/W1998767819","https://openalex.org/W1999118478","https://openalex.org/W2008708467","https://openalex.org/W2010818132","https://openalex.org/W2042426245","https://openalex.org/W2047672715","https://openalex.org/W2064712921","https://openalex.org/W2068618715","https://openalex.org/W2089989707","https://openalex.org/W2092920038","https://openalex.org/W2096699854","https://openalex.org/W2096945460","https://openalex.org/W2100805904","https://openalex.org/W2100827887","https://openalex.org/W2103017472","https://openalex.org/W2103404876","https://openalex.org/W2103525038","https://openalex.org/W2104804534","https://openalex.org/W2105686031","https://openalex.org/W2105924489","https://openalex.org/W2107644675","https://openalex.org/W2107686700","https://openalex.org/W2110181121","https://openalex.org/W2116062594","https://openalex.org/W2119191234","https://openalex.org/W2122664708","https://openalex.org/W2124932178","https://openalex.org/W2125463451","https://openalex.org/W2126064524","https://openalex.org/W2128413613","https://openalex.org/W2129137060","https://openalex.org/W2142757818","https://openalex.org/W2147274570","https://openalex.org/W2147863530","https://openalex.org/W2148143831","https://openalex.org/W2149730127","https://openalex.org/W2150004834","https://openalex.org/W2155806188","https://openalex.org/W2155837032","https://openalex.org/W2156125289","https://openalex.org/W2157142295","https://openalex.org/W2157658519","https://openalex.org/W2159294452","https://openalex.org/W2162172965","https://openalex.org/W2164260969","https://openalex.org/W2170700642","https://openalex.org/W2295598076","https://openalex.org/W2341232534","https://openalex.org/W2346473394","https://openalex.org/W2396908641","https://openalex.org/W2463756864","https://openalex.org/W2490135372","https://openalex.org/W2555891876","https://openalex.org/W2558091742","https://openalex.org/W2588614855","https://openalex.org/W2601860898","https://openalex.org/W2603443522","https://openalex.org/W2610582292","https://openalex.org/W2621036017","https://openalex.org/W2755464620","https://openalex.org/W2759742634","https://openalex.org/W2784470720","https://openalex.org/W2789316776","https://openalex.org/W2793851663","https://openalex.org/W2801931817","https://openalex.org/W2805827044","https://openalex.org/W2805894928","https://openalex.org/W2883294189","https://openalex.org/W2888353590","https://openalex.org/W2899750879","https://openalex.org/W2905744876","https://openalex.org/W2921079059","https://openalex.org/W2938901647","https://openalex.org/W2954633061","https://openalex.org/W2963066819","https://openalex.org/W2964050365","https://openalex.org/W2964822915","https://openalex.org/W2974377739","https://openalex.org/W2979665139","https://openalex.org/W2980502849","https://openalex.org/W2986392908","https://openalex.org/W2986404471","https://openalex.org/W2989888510","https://openalex.org/W2991059578","https://openalex.org/W2997680655","https://openalex.org/W2998913411","https://openalex.org/W3002136582","https://openalex.org/W3004496028","https://openalex.org/W3010877467","https://openalex.org/W3011081350","https://openalex.org/W3012353262","https://openalex.org/W3014208063","https://openalex.org/W3020440546","https://openalex.org/W3024017681","https://openalex.org/W3034070789","https://openalex.org/W3037403058","https://openalex.org/W3038215960","https://openalex.org/W3048343681","https://openalex.org/W3082590494","https://openalex.org/W3082862577","https://openalex.org/W3090178113","https://openalex.org/W3091108742","https://openalex.org/W3094312164","https://openalex.org/W3094567318","https://openalex.org/W3108295356","https://openalex.org/W3108989381","https://openalex.org/W3111931191","https://openalex.org/W3119372191","https://openalex.org/W3132857558","https://openalex.org/W3133088376","https://openalex.org/W3133571965","https://openalex.org/W3134020713","https://openalex.org/W3136291807","https://openalex.org/W3138002537","https://openalex.org/W3146401251","https://openalex.org/W3146944767","https://openalex.org/W3156959996","https://openalex.org/W3164644719","https://openalex.org/W3185165902","https://openalex.org/W3192109225","https://openalex.org/W3200607617","https://openalex.org/W3202924278","https://openalex.org/W3205926919","https://openalex.org/W3207838037","https://openalex.org/W3209094369","https://openalex.org/W3213184710","https://openalex.org/W3213853244","https://openalex.org/W4200212648","https://openalex.org/W4206144632","https://openalex.org/W4206316880","https://openalex.org/W4210323379","https://openalex.org/W4210446008","https://openalex.org/W4210810268","https://openalex.org/W4213345021","https://openalex.org/W4220742882","https://openalex.org/W4243610423","https://openalex.org/W4252329797","https://openalex.org/W4292979048","https://openalex.org/W4295765292","https://openalex.org/W4296670371","https://openalex.org/W4297256139","https://openalex.org/W4320489616","https://openalex.org/W4323066423","https://openalex.org/W4324018414","https://openalex.org/W4361001942","https://openalex.org/W4362496760","https://openalex.org/W4366606495","https://openalex.org/W4377966839","https://openalex.org/W4383313479","https://openalex.org/W4389776120","https://openalex.org/W4390346524","https://openalex.org/W4390562145","https://openalex.org/W4391483046","https://openalex.org/W4396809860","https://openalex.org/W4400747675","https://openalex.org/W4404516238","https://openalex.org/W4408389334","https://openalex.org/W4410850272","https://openalex.org/W4413621217","https://openalex.org/W4415609360","https://openalex.org/W4415826752"],"related_works":[],"abstract_inverted_index":{"Post-translational":[0],"modifications":[1],"(PTMs)":[2],"of":[3,18,41,48,113],"proteins":[4],"are":[5,27],"essential":[6],"for":[7,31,51,60,92],"cellular":[8],"function.":[9],"Owing":[10],"to":[11,110],"the":[12,42,46,57,94,111,117],"high":[13],"cost":[14],"and":[15,23,75,108],"time":[16],"demands":[17],"high-throughput":[19],"sequencing,":[20],"machine":[21],"learning":[22,25],"deep":[24],"methods":[26],"being":[28],"rapidly":[29],"developed":[30],"predicting":[32,52],"PTM":[33,53,96,106],"sites.":[34,54],"This":[35,78],"manuscript":[36],"presents":[37],"a":[38],"comprehensive":[39,103],"review":[40,79,101],"current":[43],"research":[44,84],"on":[45,65,105],"application":[47],"intelligent":[49,66],"algorithms":[50],"It":[55],"outlines":[56],"key":[58],"steps":[59],"identifying":[61],"modified":[62],"sites":[63],"based":[64],"algorithms,":[67],"including":[68],"data":[69],"pre-processing,":[70],"feature":[71],"extraction,":[72],"dimension":[73],"reduction,":[74],"classifier":[76],"development.":[77],"also":[80],"discusses":[81],"potential":[82],"future":[83],"directions":[85],"in":[86,116],"this":[87,100],"field,":[88],"providing":[89],"valuable":[90],"insights":[91],"advancing":[93],"state-of-the-art":[95],"site":[97],"prediction.":[98],"Collectively,":[99],"provides":[102],"knowledge":[104],"identification":[107],"contributes":[109],"development":[112],"advanced":[114],"predictors":[115],"future.":[118]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-11-25T00:00:00"}
