{"id":"https://openalex.org/W2916884115","doi":"https://doi.org/10.1093/database/baz024","title":"PKAD: a database of experimentally measured pKa values of ionizable groups in proteins","display_name":"PKAD: a database of experimentally measured pKa values of ionizable groups in proteins","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2916884115","doi":"https://doi.org/10.1093/database/baz024","mag":"2916884115","pmid":"https://pubmed.ncbi.nlm.nih.gov/30805645"},"language":"en","primary_location":{"id":"doi:10.1093/database/baz024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baz024","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baz024/27977586/baz024.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","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/database/article-pdf/doi/10.1093/database/baz024/27977586/baz024.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087472507","display_name":"Swagata Pahari","orcid":"https://orcid.org/0000-0001-9192-9250"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Swagata Pahari","raw_affiliation_strings":["Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069265168","display_name":"Lexuan Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lexuan Sun","raw_affiliation_strings":["Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA","institution_ids":["https://openalex.org/I8078737"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075727451","display_name":"Emil Alexov","orcid":"https://orcid.org/0000-0001-5346-0156"},"institutions":[{"id":"https://openalex.org/I8078737","display_name":"Clemson University","ror":"https://ror.org/037s24f05","country_code":"US","type":"education","lineage":["https://openalex.org/I8078737"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Emil Alexov","raw_affiliation_strings":["Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, South Carolina, USA","institution_ids":["https://openalex.org/I8078737"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5075727451"],"corresponding_institution_ids":["https://openalex.org/I8078737"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":6.1547,"has_fulltext":true,"cited_by_count":170,"citation_normalized_percentile":{"value":0.97544331,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"2019","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.7334557771682739},{"id":"https://openalex.org/keywords/protein-methods","display_name":"Protein methods","score":0.5863618850708008},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5588560700416565},{"id":"https://openalex.org/keywords/amino-acid-residue","display_name":"Amino acid residue","score":0.5146175622940063},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5068362355232239},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4933742582798004},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4905170798301697},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.4594039022922516},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.3647347092628479},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.26312148571014404},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2601771950721741},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.20936891436576843},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.18275943398475647}],"concepts":[{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.7334557771682739},{"id":"https://openalex.org/C111364199","wikidata":"https://www.wikidata.org/wiki/Q2915896","display_name":"Protein methods","level":4,"score":0.5863618850708008},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5588560700416565},{"id":"https://openalex.org/C2994376932","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Amino acid residue","level":4,"score":0.5146175622940063},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5068362355232239},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4933742582798004},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4905170798301697},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.4594039022922516},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.3647347092628479},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.26312148571014404},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2601771950721741},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.20936891436576843},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.18275943398475647},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013499","descriptor_name":"Surface Properties","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},{"descriptor_ui":"D050505","descriptor_name":"Mutant Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050505","descriptor_name":"Mutant Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D050505","descriptor_name":"Mutant Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/database/baz024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baz024","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baz024/27977586/baz024.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},{"id":"pmid:30805645","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30805645","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:europepmc.org:5386994","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6389863","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6389863","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6389863","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":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baz024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baz024","pdf_url":"https://academic.oup.com/database/article-pdf/doi/10.1093/database/baz024/27977586/baz024.pdf","source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["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":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3233386537","display_name":null,"funder_award_id":"R01GM093937","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4103095273","display_name":"Maintenance and development of DelPhi and associated resources","funder_award_id":"2r01gm093937-10a1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2916884115.pdf","grobid_xml":"https://content.openalex.org/works/W2916884115.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W144583103","https://openalex.org/W1968733906","https://openalex.org/W1970683586","https://openalex.org/W1986462587","https://openalex.org/W1994105222","https://openalex.org/W1997108100","https://openalex.org/W2003013170","https://openalex.org/W2006975013","https://openalex.org/W2015074746","https://openalex.org/W2021534482","https://openalex.org/W2032145697","https://openalex.org/W2035771816","https://openalex.org/W2039134287","https://openalex.org/W2040426346","https://openalex.org/W2045110975","https://openalex.org/W2047039535","https://openalex.org/W2050748384","https://openalex.org/W2068153876","https://openalex.org/W2076407822","https://openalex.org/W2080002005","https://openalex.org/W2086455899","https://openalex.org/W2087860563","https://openalex.org/W2091664813","https://openalex.org/W2120725832","https://openalex.org/W2126793581","https://openalex.org/W2130479394","https://openalex.org/W2131713387","https://openalex.org/W2133558724","https://openalex.org/W2152997175","https://openalex.org/W2156335429","https://openalex.org/W2157538153","https://openalex.org/W2212681463","https://openalex.org/W2315687051","https://openalex.org/W4211114880","https://openalex.org/W6654336416"],"related_works":["https://openalex.org/W2463249305","https://openalex.org/W2080876451","https://openalex.org/W2103132055","https://openalex.org/W2098429244","https://openalex.org/W4229331784","https://openalex.org/W2804651207","https://openalex.org/W2160236872","https://openalex.org/W2778886497","https://openalex.org/W2754500356","https://openalex.org/W1892752174"],"abstract_inverted_index":{"Ionizable":[0],"residues":[1,27,44,52],"play":[2],"key":[3],"roles":[4],"in":[5,29,45,53],"many":[6],"biological":[7],"phenomena":[8],"including":[9],"protein":[10,26],"folding,":[11],"enzyme":[12],"catalysis":[13],"and":[14,49,66,96,113,122,136],"binding.":[15],"We":[16],"present":[17],"PKAD,":[18],"a":[19,80,91],"database":[20,38,71,86],"of":[21,25,58,98,124],"experimentally":[22],"measured":[23],"pKas":[24,127],"reported":[28],"the":[30,110,125],"literature":[31],"or":[32],"taken":[33,108],"from":[34,109],"existing":[35],"databases.":[36],"The":[37,70,84,102],"contains":[39],"pKa":[40],"data":[41],"for":[42,50,62,94,119],"1350":[43],"157":[46],"wild-type":[47],"proteins":[48],"232":[51],"45":[54],"mutant":[55],"proteins.":[56],"Most":[57],"these":[59],"values":[60],"are":[61],"Asp,":[63],"Glu,":[64],"His":[65],"Lys":[67],"amino":[68,114,133],"acids.":[69],"is":[72],"available":[73],"as":[74,77,79,90],"downloadable":[75],"file":[76],"well":[78],"web":[81,103],"server":[82,104],"(http://compbio.clemson.edu/pkad).":[83],"PKAD":[85],"can":[87],"be":[88],"used":[89],"benchmarking":[92],"source":[93],"development":[95],"improvement":[97],"pKa's":[99],"prediction":[100],"methods.":[101],"provides":[105],"additional":[106],"information":[107],"corresponding":[111],"structures":[112],"acid":[115,134],"sequences,":[116],"which":[117],"allows":[118],"easy":[120],"search":[121],"grouping":[123],"experimental":[126],"according":[128],"to":[129],"various":[130],"biophysical":[131],"characteristics,":[132],"type":[135],"others.":[137]},"counts_by_year":[{"year":2026,"cited_by_count":16},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":22},{"year":2023,"cited_by_count":30},{"year":2022,"cited_by_count":38},{"year":2021,"cited_by_count":26},{"year":2020,"cited_by_count":15},{"year":2019,"cited_by_count":2}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
