{"id":"https://openalex.org/W7155413925","doi":"https://doi.org/10.1093/bioinformatics/btag190","title":"StrucPTM: a database of structurally validated protein modifications and their conformational variation","display_name":"StrucPTM: a database of structurally validated protein modifications and their conformational variation","publication_year":2026,"publication_date":"2026-04-18","ids":{"openalex":"https://openalex.org/W7155413925","doi":"https://doi.org/10.1093/bioinformatics/btag190","pmid":"https://pubmed.ncbi.nlm.nih.gov/42024582"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag190","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag190","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag190","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5134409699","display_name":"Seong-gwang Jeon","orcid":null},"institutions":[{"id":"https://openalex.org/I4575257","display_name":"Hanyang University","ror":"https://ror.org/046865y68","country_code":"KR","type":"education","lineage":["https://openalex.org/I4575257"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Seong-gwang Jeon","raw_affiliation_strings":["Department of Computer Science, Hanyang University , Seoul, 04763,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hanyang University , Seoul, 04763,","institution_ids":["https://openalex.org/I4575257"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008976394","display_name":"Jejoong Yoo","orcid":"https://orcid.org/0000-0001-7120-8464"},"institutions":[{"id":"https://openalex.org/I125608817","display_name":"Korea Institute for Advanced Study","ror":"https://ror.org/041hz9568","country_code":"KR","type":"facility","lineage":["https://openalex.org/I125608817"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jejoong Yoo","raw_affiliation_strings":["School of Computational Sciences, Korea Institute for Advanced Study , Seoul, 02455,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computational Sciences, Korea Institute for Advanced Study , Seoul, 02455,","institution_ids":["https://openalex.org/I125608817"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025114921","display_name":"Keehyoung Joo","orcid":"https://orcid.org/0000-0002-4612-0927"},"institutions":[{"id":"https://openalex.org/I125608817","display_name":"Korea Institute for Advanced Study","ror":"https://ror.org/041hz9568","country_code":"KR","type":"facility","lineage":["https://openalex.org/I125608817"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Keehyoung Joo","raw_affiliation_strings":["Center for Advanced Computation, Korea Institute for Advanced Study , Seoul, 02455,"],"raw_orcid":"https://orcid.org/0000-0002-4612-0927","affiliations":[{"raw_affiliation_string":"Center for Advanced Computation, Korea Institute for Advanced Study , Seoul, 02455,","institution_ids":["https://openalex.org/I125608817"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082966786","display_name":"Eunok Paek","orcid":"https://orcid.org/0000-0003-3655-9749"},"institutions":[{"id":"https://openalex.org/I4575257","display_name":"Hanyang University","ror":"https://ror.org/046865y68","country_code":"KR","type":"education","lineage":["https://openalex.org/I4575257"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Eunok Paek","raw_affiliation_strings":["Department of Computer Science, Hanyang University , Seoul, 04763,"],"raw_orcid":"https://orcid.org/0000-0003-3655-9749","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hanyang University , Seoul, 04763,","institution_ids":["https://openalex.org/I4575257"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5082966786"],"corresponding_institution_ids":["https://openalex.org/I4575257"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.52195365,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.11779999732971191,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.11779999732971191,"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/T13157","display_name":"Cancer-related gene regulation","score":0.11729999631643295,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.09260000288486481,"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/uniprot","display_name":"UniProt","score":0.9050999879837036},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.5708000063896179},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5418999791145325},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.4984000027179718},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.45680001378059387},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.4422999918460846},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4408000111579895},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.4059999883174896},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.3610999882221222}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.9050999879837036},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6793000102043152},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.5708000063896179},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5418999791145325},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5375000238418579},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.4984000027179718},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.45680001378059387},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.4422999918460846},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4408000111579895},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42910000681877136},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.4059999883174896},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3684000074863434},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.3610999882221222},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.3578000068664551},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35659998655319214},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.3508000075817108},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.3476000130176544},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.32690000534057617},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3075000047683716},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.3061999976634979},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.30300000309944153},{"id":"https://openalex.org/C100631289","wikidata":"https://www.wikidata.org/wiki/Q898362","display_name":"Posttranslational modification","level":3,"score":0.299699991941452},{"id":"https://openalex.org/C69131567","wikidata":"https://www.wikidata.org/wiki/Q2068215","display_name":"Structural bioinformatics","level":3,"score":0.2964000105857849},{"id":"https://openalex.org/C4668613","wikidata":"https://www.wikidata.org/wiki/Q4116110","display_name":"Structural alignment","level":5,"score":0.2847000062465668},{"id":"https://openalex.org/C111364199","wikidata":"https://www.wikidata.org/wiki/Q2915896","display_name":"Protein methods","level":4,"score":0.28060001134872437},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.2777999937534332},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.2777999937534332},{"id":"https://openalex.org/C58773245","wikidata":"https://www.wikidata.org/wiki/Q4832556","display_name":"Structural Classification of Proteins database","level":3,"score":0.2718000113964081},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2712000012397766},{"id":"https://openalex.org/C20901353","wikidata":"https://www.wikidata.org/wiki/Q4117139","display_name":"Biological database","level":2,"score":0.2596000134944916},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.2547999918460846},{"id":"https://openalex.org/C147816474","wikidata":"https://www.wikidata.org/wiki/Q169525","display_name":"Protein engineering","level":3,"score":0.251800000667572}],"mesh":[{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag190","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag190","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42024582","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42024582","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:13138842","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13138842/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag190","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag190","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","score":0.537226140499115,"display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W2008708467","https://openalex.org/W2031772330","https://openalex.org/W2097356092","https://openalex.org/W2102245393","https://openalex.org/W2106235286","https://openalex.org/W2114850508","https://openalex.org/W2140047797","https://openalex.org/W2164018321","https://openalex.org/W2620998958","https://openalex.org/W2900674118","https://openalex.org/W2901496107","https://openalex.org/W3202924278","https://openalex.org/W4280512557","https://openalex.org/W4404225847","https://openalex.org/W4404458588","https://openalex.org/W4415516474"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Post-translational":[1],"modifications":[2,31],"(PTMs)":[3],"alter":[4],"functional":[5],"states":[6],"and":[7,26,47,66,122,142,178,190,199],"interaction":[8],"specificity":[9],"largely":[10],"through":[11,182],"the":[12,81,124,136],"conformational":[13,159],"changes":[14],"they":[15],"impose":[16],"on":[17,148,195],"protein":[18,54,63],"structure.":[19],"However,":[20],"most":[21],"existing":[22],"resources":[23],"remain":[24],"sequence-centric":[25],"cannot":[27],"reveal":[28],"how":[29],"chemical":[30],"reshape":[32],"3D":[33,176],"structures.":[34],"To":[35],"address":[36],"this":[37],"gap,":[38],"we":[39],"propose":[40],"a":[41,57,73,104],"structural":[42,114,153,180],"database":[43,74,108],"that":[44,75],"systematically":[45],"extracts":[46,76],"contextualizes":[48],"modification":[49,100],"sites":[50],"within":[51],"experimentally":[52],"determined":[53],"structures,":[55],"providing":[56],"foundation":[58],"for":[59],"future":[60],"studies":[61],"of":[62],"structure,":[64,117],"function,":[65],"regulatory":[67],"mechanisms.":[68],"RESULTS:":[69],"We":[70],"present":[71],"StrucPTM,":[72],"modified":[77],"residues":[78,111],"directly":[79],"from":[80,164],"Protein":[82],"Data":[83],"Bank":[84],"(PDB)":[85],"structures":[86],"using":[87,112],"atom-level":[88],"composition":[89],"rules,":[90],"substantially":[91],"expanding":[92],"coverage":[93],"beyond":[94],"annotation-dependent":[95],"methods.":[96],"Each":[97],"validated":[98],"PTM":[99,125],"is":[101],"mapped":[102],"onto":[103],"UniProt":[105,138],"entry.":[106],"The":[107,187],"further":[109],"characterizes":[110],"key":[113],"descriptors-including":[115],"secondary":[116],"relative":[118],"solvent":[119],"accessibility":[120],"(RSA),":[121],"whether":[123],"site":[126],"lies":[127],"at":[128],"an":[129],"interchain":[130],"interface.":[131],"All":[132],"chains":[133],"associated":[134],"with":[135],"same":[137],"ID":[139],"are":[140,192,200],"compared":[141],"grouped":[143],"into":[144],"homolog":[145],"sets":[146],"based":[147],"sequence":[149,166],"identity.":[150],"This":[151],"emphasizes":[152],"conservation":[154],"among":[155],"homologs,":[156],"allowing":[157],"PTM-induced":[158],"deviations":[160],"to":[161],"be":[162],"distinguished":[163],"unrelated":[165],"divergence.":[167],"AVAILABILITY":[168],"AND":[169],"IMPLEMENTATION:":[170],"StrucPTM":[171],"offers":[172],"searchable":[173],"access,":[174],"interactive":[175],"visualization,":[177],"homolog-based":[179],"comparison":[181],"its":[183],"web":[184],"interface:":[185],"https://prix.hanyang.ac.kr/strucptm.":[186],"source":[188],"code":[189],"datasets":[191],"permanently":[193],"archived":[194],"Zenodo":[196],"(DOI:":[197],"10.5281/zenodo.18939125)":[198],"accessible":[201],"via":[202],"GitHub":[203],"(https://github.com/HanyangBISLab/StrucPTM.git).":[204]},"counts_by_year":[],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2026-04-24T00:00:00"}
