{"id":"https://openalex.org/W4320489616","doi":"https://doi.org/10.1093/bib/bbad052","title":"PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk","display_name":"PPICT: an integrated deep neural network for predicting inter-protein PTM cross-talk","publication_year":2023,"publication_date":"2023-02-13","ids":{"openalex":"https://openalex.org/W4320489616","doi":"https://doi.org/10.1093/bib/bbad052","pmid":"https://pubmed.ncbi.nlm.nih.gov/36781207"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad052","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad052/49560544/bbad052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad052/49560544/bbad052.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074124642","display_name":"Fei Zhu","orcid":"https://orcid.org/0000-0002-2226-2859"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]},{"id":"https://openalex.org/I4210122727","display_name":"Suzhou Institute of Systems Medicine","ror":"https://ror.org/02szepc22","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210122727","https://openalex.org/I4210141683"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Zhu","raw_affiliation_strings":["Center for Systems Biology , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","School of Computer Science and Technology, Soochow University , 215006, Suzhou , China","Soochow University , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Systems Biology , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","institution_ids":["https://openalex.org/I4210122727"]},{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University , 215006, Suzhou , China","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"Soochow University , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043924119","display_name":"Lei Deng","orcid":"https://orcid.org/0000-0002-2395-6334"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Deng","raw_affiliation_strings":["School of Computer Science and Technology, Soochow University , 215006, Suzhou , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University , 215006, Suzhou , China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039184750","display_name":"Yuhao Dai","orcid":"https://orcid.org/0009-0001-7836-5523"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuhao Dai","raw_affiliation_strings":["School of Computer Science and Technology, Soochow University , 215006, Suzhou , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University , 215006, Suzhou , China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100446002","display_name":"Guangyu Zhang","orcid":"https://orcid.org/0000-0002-1176-292X"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guangyu Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Soochow University , 215006, Suzhou , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Soochow University , 215006, Suzhou , China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003989655","display_name":"Fanwang Meng","orcid":"https://orcid.org/0000-0003-2886-7012"},"institutions":[{"id":"https://openalex.org/I98251732","display_name":"McMaster University","ror":"https://ror.org/02fa3aq29","country_code":"CA","type":"education","lineage":["https://openalex.org/I98251732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Fanwang Meng","raw_affiliation_strings":["Department of Chemistry and Chemical Biology, McMaster University , L8S 4L8, Ontario , Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Chemical Biology, McMaster University , L8S 4L8, Ontario , Canada","institution_ids":["https://openalex.org/I98251732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024637740","display_name":"Cheng Luo","orcid":"https://orcid.org/0000-0003-3864-8382"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Luo","raw_affiliation_strings":["Chinese Academy of Sciences , Shanghai Institute of Materia Medica, , 201203, Shanghai , China","State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, , 201203, Shanghai , China","State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences , Shanghai Institute of Materia Medica, , 201203, Shanghai , China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]},{"raw_affiliation_string":"State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, , 201203, Shanghai , China","institution_ids":["https://openalex.org/I4210112820"]},{"raw_affiliation_string":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101617943","display_name":"Guang Hu","orcid":"https://orcid.org/0000-0002-8754-1541"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]},{"id":"https://openalex.org/I4210122727","display_name":"Suzhou Institute of Systems Medicine","ror":"https://ror.org/02szepc22","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210122727","https://openalex.org/I4210141683"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guang Hu","raw_affiliation_strings":["Center for Systems Biology , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","Soochow University , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Systems Biology , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","institution_ids":["https://openalex.org/I4210122727"]},{"raw_affiliation_string":"Soochow University , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045167053","display_name":"Zhongjie Liang","orcid":"https://orcid.org/0000-0003-0763-5407"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]},{"id":"https://openalex.org/I4210112820","display_name":"Shanghai Institute of Materia Medica","ror":"https://ror.org/022syn853","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112820"]},{"id":"https://openalex.org/I4210122727","display_name":"Suzhou Institute of Systems Medicine","ror":"https://ror.org/02szepc22","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210122727","https://openalex.org/I4210141683"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhongjie Liang","raw_affiliation_strings":["Center for Systems Biology , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","Chinese Academy of Sciences , Shanghai Institute of Materia Medica, , 201203, Shanghai , China","Key Laboratory of Systems Biomedicine (Ministry of Education) , Center for Systems Biomedicine, , 200240, Shanghai , China","Shanghai Jiao Tong University , Center for Systems Biomedicine, , 200240, Shanghai , China","Soochow University , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, , 201203, Shanghai , China","State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China","Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China","Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Systems Biology , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","institution_ids":["https://openalex.org/I4210122727"]},{"raw_affiliation_string":"Chinese Academy of Sciences , Shanghai Institute of Materia Medica, , 201203, Shanghai , China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Key Laboratory of Systems Biomedicine (Ministry of Education) , Center for Systems Biomedicine, , 200240, Shanghai , China","institution_ids":[]},{"raw_affiliation_string":"Shanghai Jiao Tong University , Center for Systems Biomedicine, , 200240, Shanghai , China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Soochow University , Department of Bioinformatics, School of Biology and Basic Medical Sciences, , 215123, Suzhou , China","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, , 201203, Shanghai , China","institution_ids":["https://openalex.org/I4210112820"]},{"raw_affiliation_string":"State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China","institution_ids":["https://openalex.org/I4210112820","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, 215123, Suzhou, China","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"Key Laboratory of Systems Biomedicine (Ministry of Education), Center for Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5045167053","https://openalex.org/A5101617943"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I19820366","https://openalex.org/I3923682","https://openalex.org/I4210112820","https://openalex.org/I4210122727"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.2811,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.89657701,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"24","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9991000294685364,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9991000294685364,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9954000115394592,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9940999746322632,"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/computer-science","display_name":"Computer science","score":0.602320671081543},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.547267496585846},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5230311155319214},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.510139524936676},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4906679391860962},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4571857154369354},{"id":"https://openalex.org/keywords/allosteric-regulation","display_name":"Allosteric regulation","score":0.4416577219963074},{"id":"https://openalex.org/keywords/cross-validation","display_name":"Cross-validation","score":0.430225670337677},{"id":"https://openalex.org/keywords/posttranslational-modification","display_name":"Posttranslational modification","score":0.4292975962162018},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4129067063331604},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.381795197725296},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2863978147506714},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2419150173664093},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2060726284980774},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1536654829978943},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.14590105414390564},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.09794437885284424}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.602320671081543},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.547267496585846},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5230311155319214},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.510139524936676},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4906679391860962},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4571857154369354},{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.4416577219963074},{"id":"https://openalex.org/C27181475","wikidata":"https://www.wikidata.org/wiki/Q541014","display_name":"Cross-validation","level":2,"score":0.430225670337677},{"id":"https://openalex.org/C100631289","wikidata":"https://www.wikidata.org/wiki/Q898362","display_name":"Posttranslational modification","level":3,"score":0.4292975962162018},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4129067063331604},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.381795197725296},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2863978147506714},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2419150173664093},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2060726284980774},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1536654829978943},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14590105414390564},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.09794437885284424},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad052","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad052/49560544/bbad052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36781207","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36781207","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad052","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad052","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad052/49560544/bbad052.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G21622510","display_name":null,"funder_award_id":"61303108","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G24520245","display_name":null,"funder_award_id":"61303108","funder_id":"https://openalex.org/F4320322769","funder_display_name":"Natural Science Foundation of Jiangsu Province"},{"id":"https://openalex.org/G2624156301","display_name":null,"funder_award_id":"32271292","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3401316878","display_name":null,"funder_award_id":"SIMM2205KF","funder_id":"https://openalex.org/F4320335657","funder_display_name":"State Key Laboratory of Drug Research"},{"id":"https://openalex.org/G5732843278","display_name":null,"funder_award_id":"31872723","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5741616821","display_name":null,"funder_award_id":"31872723","funder_id":"https://openalex.org/F4320327518","funder_display_name":"Priority Academic Program Development of Jiangsu Higher Education Institutions"},{"id":"https://openalex.org/G644907996","display_name":null,"funder_award_id":"SIMM2205KF-11","funder_id":"https://openalex.org/F4320321133","funder_display_name":"Chinese Academy of Sciences"},{"id":"https://openalex.org/G6786688740","display_name":null,"funder_award_id":"KLSB2019KF-02","funder_id":"https://openalex.org/F4320322999","funder_display_name":"Shanghai Jiao Tong University"},{"id":"https://openalex.org/G739385085","display_name":null,"funder_award_id":"BK20211102","funder_id":"https://openalex.org/F4320322769","funder_display_name":"Natural Science Foundation of Jiangsu Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"},{"id":"https://openalex.org/F4320321605","display_name":"Government of Jiangsu Province","ror":"https://ror.org/004svx814"},{"id":"https://openalex.org/F4320322769","display_name":"Natural Science Foundation of Jiangsu Province","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322999","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04"},{"id":"https://openalex.org/F4320327518","display_name":"Priority Academic Program Development of Jiangsu Higher Education Institutions","ror":null},{"id":"https://openalex.org/F4320335657","display_name":"State Key Laboratory of Drug Research","ror":null},{"id":"https://openalex.org/F4320335988","display_name":"Shanghai Institute of Materia Medica, Chinese Academy of Sciences","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4320489616.pdf"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W51274325","https://openalex.org/W1972378799","https://openalex.org/W1995254028","https://openalex.org/W2022922908","https://openalex.org/W2033208312","https://openalex.org/W2048934130","https://openalex.org/W2056127109","https://openalex.org/W2057616220","https://openalex.org/W2095926488","https://openalex.org/W2103388612","https://openalex.org/W2105869859","https://openalex.org/W2116062594","https://openalex.org/W2122196090","https://openalex.org/W2135197754","https://openalex.org/W2156916536","https://openalex.org/W2158217645","https://openalex.org/W2158577092","https://openalex.org/W2164018321","https://openalex.org/W2393319904","https://openalex.org/W2424755250","https://openalex.org/W2563212203","https://openalex.org/W2744003029","https://openalex.org/W2748559592","https://openalex.org/W2768826694","https://openalex.org/W2788917583","https://openalex.org/W2800934160","https://openalex.org/W2802147764","https://openalex.org/W2894836881","https://openalex.org/W2901496107","https://openalex.org/W2906675418","https://openalex.org/W2914195316","https://openalex.org/W2917858269","https://openalex.org/W2924293762","https://openalex.org/W2952533623","https://openalex.org/W2970416468","https://openalex.org/W2986268970","https://openalex.org/W3004392625","https://openalex.org/W3016841005","https://openalex.org/W3022910488","https://openalex.org/W3046468150","https://openalex.org/W3100951629","https://openalex.org/W3107527779","https://openalex.org/W3116613266","https://openalex.org/W3119395971","https://openalex.org/W3134718897","https://openalex.org/W3136918052","https://openalex.org/W3140562424","https://openalex.org/W3146401251","https://openalex.org/W3157357317","https://openalex.org/W3164662270","https://openalex.org/W3185245858","https://openalex.org/W3187251571","https://openalex.org/W3191137525","https://openalex.org/W3199280095","https://openalex.org/W3207678186","https://openalex.org/W4206922377","https://openalex.org/W4220831425","https://openalex.org/W4283313464","https://openalex.org/W4285007839","https://openalex.org/W4285266698","https://openalex.org/W4288095686","https://openalex.org/W6768553266","https://openalex.org/W6807788437","https://openalex.org/W6809271837"],"related_works":["https://openalex.org/W2939998722","https://openalex.org/W2169750653","https://openalex.org/W2195592873","https://openalex.org/W1971782741","https://openalex.org/W3005062988","https://openalex.org/W2075777827","https://openalex.org/W4211217675","https://openalex.org/W2592466923","https://openalex.org/W1555254413","https://openalex.org/W4231759675"],"abstract_inverted_index":{"Post-translational":[0],"modifications":[1,23],"(PTMs)":[2],"fine-tune":[3],"various":[4],"signaling":[5],"pathways":[6,221],"not":[7],"only":[8],"by":[9,18,86,223],"the":[10,19,60,120,141,152,158,168,173,178,184,209,214],"modification":[11],"of":[12,21,119,144,165],"a":[13,36,70,133],"single":[14],"residue,":[15],"but":[16],"also":[17],"interplay":[20],"different":[22,219],"on":[24,188],"residue":[25,49],"pairs":[26,50],"within":[27],"or":[28],"between":[29,123,206,218],"proteins,":[30],"defined":[31],"as":[32],"PTM":[33,45,64,79,84,180,194,204],"cross-talk.":[34],"As":[35],"challenging":[37],"question,":[38],"less":[39],"attention":[40],"has":[41],"been":[42],"given":[43],"to":[44],"dynamics":[46],"underlying":[47,54],"cross-talk":[48,85,100,205,217],"and":[51,91,109,126,129,191,212],"structural":[52,92],"information":[53,90,93],"protein-protein":[55],"interaction":[56],"(PPI)":[57],"graph,":[58],"limiting":[59],"progress":[61],"in":[62,112,140,183],"this":[63],"functional":[65,185],"research.":[66],"Here":[67],"we":[68],"propose":[69],"novel":[71],"integrated":[72],"deep":[73],"neural":[74],"network":[75],"PPICT":[76,154,174,197],"(Predictor":[77],"for":[78,94,202,216],"Inter-protein":[80],"Cross-Talk),":[81],"which":[82],"predicts":[83],"combining":[87],"protein":[88,124,130],"sequence-structure-dynamics":[89],"PPI":[95],"graph.":[96],"We":[97],"find":[98],"that":[99,151],"events":[101],"preferentially":[102],"occur":[103],"among":[104],"residues":[105],"with":[106,161],"high":[107,110],"co-evolution":[108],"potential":[111,179],"allosteric":[113],"regulation.":[114],"To":[115],"make":[116],"full":[117],"use":[118],"complex":[121],"associations":[122],"evolutionary":[125],"biophysical":[127],"features,":[128,132],"pair":[131],"heterogeneous":[134],"feature":[135],"combination":[136],"net":[137],"is":[138],"introduced":[139,222],"final":[142],"prediction":[143,159],"PPICT.":[145],"The":[146],"comprehensive":[147],"test":[148],"results":[149],"show":[150],"proposed":[153],"method":[155,175],"significantly":[156],"improves":[157],"performance":[160],"an":[162,199],"AUC":[163],"value":[164],"0.869,":[166],"outperforming":[167],"existing":[169],"state-of-the-art":[170],"methods.":[171],"Additionally,":[172],"can":[176],"capture":[177],"cross-talks":[181],"involved":[182],"regulatory":[186],"PTMs":[187],"modifying":[189],"enzymes":[190],"their":[192],"catalyzed":[193],"substrates.":[195],"Therefore,":[196],"represents":[198],"effective":[200],"tool":[201],"identifying":[203],"proteins":[207],"at":[208],"proteome":[210],"level":[211],"highlights":[213],"hints":[215],"signal":[220],"PTMs.":[224]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-05-21T09:19:25.381259","created_date":"2025-10-10T00:00:00"}
