{"id":"https://openalex.org/W2095926488","doi":"https://doi.org/10.1093/nar/gku1081","title":"PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins","display_name":"PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins","publication_year":2014,"publication_date":"2014-10-31","ids":{"openalex":"https://openalex.org/W2095926488","doi":"https://doi.org/10.1093/nar/gku1081","mag":"2095926488","pmid":"https://pubmed.ncbi.nlm.nih.gov/25361965"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gku1081","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku1081","pdf_url":"https://academic.oup.com/nar/article-pdf/43/D1/D494/17436284/gku1081.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","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/nar/article-pdf/43/D1/D494/17436284/gku1081.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028520416","display_name":"Pablo M\u00ednguez","orcid":"https://orcid.org/0000-0003-4099-9421"},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Pablo Minguez","raw_affiliation_strings":["European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany","institution_ids":["https://openalex.org/I4210153543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072645674","display_name":"Ivica Letuni\u0107","orcid":"https://orcid.org/0000-0003-3560-4288"},"institutions":[{"id":"https://openalex.org/I4210107206","display_name":"Biobyte Solutions (Germany)","ror":"https://ror.org/01r8nn991","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210107206"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ivica Letunic","raw_affiliation_strings":["Biobyte solutions GmbH, Bothestr 142, 69117 Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-3560-4288","affiliations":[{"raw_affiliation_string":"Biobyte solutions GmbH, Bothestr 142, 69117 Heidelberg, Germany","institution_ids":["https://openalex.org/I4210107206"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057527967","display_name":"Luca Parca","orcid":"https://orcid.org/0000-0002-0924-8518"},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Luca Parca","raw_affiliation_strings":["European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany","institution_ids":["https://openalex.org/I4210153543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008521472","display_name":"Luz Garc\u00eda\u2010Alonso","orcid":null},"institutions":[{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Luz Garcia-Alonso","raw_affiliation_strings":["Computational Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain","institution_ids":["https://openalex.org/I4210165109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074140420","display_name":"Joaqu\u0131\u0301n Dopazo","orcid":"https://orcid.org/0000-0003-3318-120X"},"institutions":[{"id":"https://openalex.org/I4210165109","display_name":"Centro de Investigacion Principe Felipe","ror":"https://ror.org/05xr2yq54","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210165109"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Joaquin Dopazo","raw_affiliation_strings":["Computational Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Genomics Department, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe (CIPF), Valencia, Spain","institution_ids":["https://openalex.org/I4210165109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050318013","display_name":"Jaime Huerta\u2010Cepas","orcid":"https://orcid.org/0000-0003-4195-5025"},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jaime Huerta-Cepas","raw_affiliation_strings":["European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany","institution_ids":["https://openalex.org/I4210153543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074309419","display_name":"Peer Bork","orcid":"https://orcid.org/0000-0002-2627-833X"},"institutions":[{"id":"https://openalex.org/I205582932","display_name":"Max Delbr\u00fcck Center","ror":"https://ror.org/04p5ggc03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I205582932"]},{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]},{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Peer Bork","raw_affiliation_strings":["European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany Max-Delbruck-Centre for Molecular Medicine, Berlin-Buch, Germany bork@embl.de","Max-Delbruck-Centre for Molecular Medicine, Berlin-Buch, Germany","European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany Max-Delbruck-Centre for Molecular Medicine, Berlin-Buch, Germany bork@embl.de","institution_ids":["https://openalex.org/I4210153543","https://openalex.org/I205582932","https://openalex.org/I4210138560"]},{"raw_affiliation_string":"Max-Delbruck-Centre for Molecular Medicine, Berlin-Buch, Germany","institution_ids":["https://openalex.org/I205582932"]},{"raw_affiliation_string":"European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany","institution_ids":["https://openalex.org/I4210153543"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5074309419"],"corresponding_institution_ids":["https://openalex.org/I205582932","https://openalex.org/I4210138560","https://openalex.org/I4210153543"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":7.5009,"has_fulltext":true,"cited_by_count":112,"citation_normalized_percentile":{"value":0.97666868,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"43","issue":"D1","first_page":"D494","last_page":"D502"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9891999959945679,"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"}},"topics":[{"id":"https://openalex.org/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.9891999959945679,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9883999824523926,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.9850999712944031,"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/posttranslational-modification","display_name":"Posttranslational modification","score":0.8077316284179688},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7766761779785156},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.7094476819038391},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.6367456316947937},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5262224674224854},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.42847979068756104},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3322190046310425},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31082451343536377},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2412351369857788},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12604498863220215}],"concepts":[{"id":"https://openalex.org/C100631289","wikidata":"https://www.wikidata.org/wiki/Q898362","display_name":"Posttranslational modification","level":3,"score":0.8077316284179688},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7766761779785156},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.7094476819038391},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.6367456316947937},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5262224674224854},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.42847979068756104},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3322190046310425},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31082451343536377},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2412351369857788},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12604498863220215},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[{"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","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":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gku1081","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku1081","pdf_url":"https://academic.oup.com/nar/article-pdf/43/D1/D494/17436284/gku1081.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:25361965","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25361965","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:edoc.mdc-berlin.de:14414","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400224","display_name":"MDC Repository (Max-Delbrueck-Center for Molecular Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:europepmc.org:3354862","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4383916","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gku1081","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gku1081","pdf_url":"https://academic.oup.com/nar/article-pdf/43/D1/D494/17436284/gku1081.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2095926488.pdf","grobid_xml":"https://content.openalex.org/works/W2095926488.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1966693725","https://openalex.org/W1972378799","https://openalex.org/W1979803040","https://openalex.org/W1980506273","https://openalex.org/W1986896225","https://openalex.org/W1993038297","https://openalex.org/W1995254028","https://openalex.org/W1995286508","https://openalex.org/W1997272729","https://openalex.org/W2005893121","https://openalex.org/W2009826707","https://openalex.org/W2014776147","https://openalex.org/W2022922908","https://openalex.org/W2023346730","https://openalex.org/W2023910541","https://openalex.org/W2030637684","https://openalex.org/W2043764521","https://openalex.org/W2044100153","https://openalex.org/W2050067448","https://openalex.org/W2052002049","https://openalex.org/W2066917111","https://openalex.org/W2075319133","https://openalex.org/W2078964925","https://openalex.org/W2087548571","https://openalex.org/W2088357489","https://openalex.org/W2100148427","https://openalex.org/W2100362259","https://openalex.org/W2101876702","https://openalex.org/W2105924489","https://openalex.org/W2118245746","https://openalex.org/W2118439154","https://openalex.org/W2120772351","https://openalex.org/W2121249690","https://openalex.org/W2122863289","https://openalex.org/W2123527017","https://openalex.org/W2127795028","https://openalex.org/W2131562240","https://openalex.org/W2133002450","https://openalex.org/W2134095164","https://openalex.org/W2147418543","https://openalex.org/W2150091336","https://openalex.org/W2153125965","https://openalex.org/W2154384871","https://openalex.org/W2155521690","https://openalex.org/W2155814768","https://openalex.org/W2157658519","https://openalex.org/W2158577092","https://openalex.org/W2162103775","https://openalex.org/W2162172965","https://openalex.org/W2169543816","https://openalex.org/W2605068739","https://openalex.org/W4206159125","https://openalex.org/W4247554111"],"related_works":["https://openalex.org/W2800730174","https://openalex.org/W4256487025","https://openalex.org/W4255644844","https://openalex.org/W2095926488","https://openalex.org/W2768732437","https://openalex.org/W1875352418","https://openalex.org/W1992223954","https://openalex.org/W2075580221","https://openalex.org/W2185789005","https://openalex.org/W1511994447"],"abstract_inverted_index":{"The":[0,145],"post-translational":[1,67,171],"regulation":[2,172],"of":[3,17,37,53,65,82,101,103,148,166,173,186],"proteins":[4,175,190],"is":[5],"mainly":[6],"driven":[7],"by":[8,14],"two":[9,26,116],"molecular":[10],"events,":[11],"their":[12,20],"modification":[13],"several":[15,88],"types":[16,168],"moieties":[18],"and":[19,30,51,57,63,94,114,176,191],"interaction":[21],"with":[22],"other":[23],"proteins.":[24,118,144],"These":[25],"processes":[27],"are":[28,32,72],"interdependent":[29],"together":[31],"responsible":[33],"for":[34,125],"the":[35,38,49,61,79,98,111,170],"function":[36],"protein":[39,66,113],"in":[40,84,110],"a":[41,132],"particular":[42],"cell":[43],"state.":[44],"Several":[45],"databases":[46],"focus":[47],"on":[48,60,77,91],"prediction":[50],"compilation":[52],"protein-protein":[54],"interactions":[55],"(PPIs)":[56],"no":[58,73],"less":[59],"collection":[62],"analysis":[64],"modifications":[68,109],"(PTMs),":[69],"however,":[70],"there":[71],"resources":[74],"that":[75,105],"concentrate":[76],"describing":[78],"regulatory":[80],"role":[81],"PTMs":[83,104,137,163,187],"PPIs.":[85,197],"We":[86],"developed":[87],"methods":[89],"based":[90],"residue":[92],"co-evolution":[93],"proximity":[95],"to":[96,108,121,135],"predict":[97],"functional":[99],"associations":[100,185],"pairs":[102],"we":[106,156,181],"apply":[107],"same":[112],"between":[115],"interacting":[117],"In":[119,179],"order":[120],"make":[122],"data":[123],"available":[124],"understudied":[126],"organisms,":[127],"PTMcode":[128,149],"v2":[129],"(http://ptmcode.embl.de)":[130],"includes":[131],"new":[133],"strategy":[134],"propagate":[136],"from":[138,154],"validated":[139],"modified":[140],"sites":[141],"through":[142],"orthologous":[143],"second":[146],"release":[147],"covers":[150],"19":[151],"eukaryotic":[152],"species":[153],"which":[155],"collected":[157],"more":[158],"than":[159],"300,000":[160],"experimentally":[161],"verified":[162],"(>1,300,000":[164],"propagated)":[165],"69":[167],"extracting":[169],">100,000":[174,177],"interactions.":[178],"total,":[180],"report":[182],"8":[183],"million":[184,194],"regulating":[188],"single":[189],"over":[192],"9.4":[193],"interplays":[195],"tuning":[196]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":18},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":11},{"year":2015,"cited_by_count":9}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}