{"id":"https://openalex.org/W1969015820","doi":"https://doi.org/10.1093/nar/gkj035","title":"PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values","display_name":"PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values","publication_year":2005,"publication_date":"2005-12-28","ids":{"openalex":"https://openalex.org/W1969015820","doi":"https://doi.org/10.1093/nar/gkj035","mag":"1969015820","pmid":"https://pubmed.ncbi.nlm.nih.gov/16381845"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkj035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj035","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D199/3923893/gkj035.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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/34/suppl_1/D199/3923893/gkj035.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051163780","display_name":"Christopher P. Toseland","orcid":"https://orcid.org/0000-0002-1641-7535"},"institutions":[{"id":"https://openalex.org/I4210153742","display_name":"Jenner Institute","ror":"https://ror.org/05kwhph67","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210153742"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"C. P. Toseland","raw_affiliation_strings":["Edward Jenner Institute for Vaccine Research Compton, Berkshire, RG20 7NN, UK","Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Edward Jenner Institute for Vaccine Research Compton, Berkshire, RG20 7NN, UK","institution_ids":[]},{"raw_affiliation_string":"Edward Jenner Institute for Vaccine Research, Compton, Berkshire RG20 7NN, UK","institution_ids":["https://openalex.org/I4210153742"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5051163780"],"corresponding_institution_ids":["https://openalex.org/I4210153742"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.1374,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.75132116,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"34","issue":"90001","first_page":"D199","last_page":"D203"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9998000264167786,"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":0.9988999962806702,"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/compendium","display_name":"Compendium","score":0.8120439648628235},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.7424479722976685},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.5437009334564209},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5370388031005859},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.5315081477165222},{"id":"https://openalex.org/keywords/database-search-engine","display_name":"Database search engine","score":0.44265180826187134},{"id":"https://openalex.org/keywords/protein-structure-database","display_name":"Protein structure database","score":0.4116829037666321},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37751537561416626},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.344176709651947},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3393293023109436},{"id":"https://openalex.org/keywords/search-engine","display_name":"Search engine","score":0.3213903307914734},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.29252779483795166},{"id":"https://openalex.org/keywords/sequence-database","display_name":"Sequence database","score":0.22336694598197937},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1950429379940033}],"concepts":[{"id":"https://openalex.org/C2778473407","wikidata":"https://www.wikidata.org/wiki/Q1459574","display_name":"Compendium","level":2,"score":0.8120439648628235},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.7424479722976685},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.5437009334564209},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5370388031005859},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.5315081477165222},{"id":"https://openalex.org/C48000682","wikidata":"https://www.wikidata.org/wiki/Q5227411","display_name":"Database search engine","level":3,"score":0.44265180826187134},{"id":"https://openalex.org/C136475424","wikidata":"https://www.wikidata.org/wiki/Q7251500","display_name":"Protein structure database","level":4,"score":0.4116829037666321},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37751537561416626},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.344176709651947},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3393293023109436},{"id":"https://openalex.org/C97854310","wikidata":"https://www.wikidata.org/wiki/Q19541","display_name":"Search engine","level":2,"score":0.3213903307914734},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.29252779483795166},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.22336694598197937},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1950429379940033},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","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":"D020407","descriptor_name":"Internet","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":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkj035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj035","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D199/3923893/gkj035.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:16381845","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16381845","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:publications.aston.ac.uk:25123","is_oa":true,"landing_page_url":"https://publications.aston.ac.uk/view/author/733e27f3bd78f1558698c7b958480e21.html>","pdf_url":"https://publications.aston.ac.uk/id/eprint/25123/1/Integrated_web_accessible_database_of_experimentally_determined_protein_pKa_values.pdf","source":{"id":"https://openalex.org/S4306400483","display_name":"Aston Publications Explorer (Aston University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I169199633","host_organization_name":"Aston University","host_organization_lineage":["https://openalex.org/I169199633"],"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":"PeerReviewed"},{"id":"pmh:oai:europepmc.org:156861","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1347398","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:kar.kent.ac.uk:47866","is_oa":false,"landing_page_url":"https://kar.kent.ac.uk/47866/","pdf_url":null,"source":{"id":"https://openalex.org/S4377196264","display_name":"Kent Academic Repository (University of Kent)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20581793","host_organization_name":"University of Kent","host_organization_lineage":["https://openalex.org/I20581793"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:1347398","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1347398","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkj035","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkj035","pdf_url":"https://academic.oup.com/nar/article-pdf/34/suppl_1/D199/3923893/gkj035.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320307773","display_name":"GlaxoSmithKline","ror":"https://ror.org/01xsqw823"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1969015820.pdf","grobid_xml":"https://content.openalex.org/works/W1969015820.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1974796899","https://openalex.org/W1984223438","https://openalex.org/W1998401012","https://openalex.org/W2004145462","https://openalex.org/W2005265312","https://openalex.org/W2021534482","https://openalex.org/W2022383019","https://openalex.org/W2031482863","https://openalex.org/W2032486811","https://openalex.org/W2040816544","https://openalex.org/W2041710436","https://openalex.org/W2049704184","https://openalex.org/W2050357762","https://openalex.org/W2050748384","https://openalex.org/W2062604077","https://openalex.org/W2064982705","https://openalex.org/W2071510805","https://openalex.org/W2079243965","https://openalex.org/W2087860563","https://openalex.org/W2119942095","https://openalex.org/W2125531202","https://openalex.org/W2130479394","https://openalex.org/W2134623266","https://openalex.org/W2148853951","https://openalex.org/W2158714788","https://openalex.org/W2167567753","https://openalex.org/W2314118227","https://openalex.org/W3195246384","https://openalex.org/W4241029978"],"related_works":["https://openalex.org/W2146442590","https://openalex.org/W4388749535","https://openalex.org/W1979707045","https://openalex.org/W4285340733","https://openalex.org/W2121688928","https://openalex.org/W4375844720","https://openalex.org/W1495233806","https://openalex.org/W2113091268","https://openalex.org/W2419335570","https://openalex.org/W1997379747"],"abstract_inverted_index":{"The":[0,51,77,136],"Protein":[1,126],"pK(a)":[2,58,74],"Database":[3],"(PPD)":[4],"v1.0":[5],"provides":[6],"a":[7,26,55,62,97],"compendium":[8],"of":[9,25,64,73,108],"protein":[10,46,57],"residue-specific":[11],"ionization":[12],"equilibria":[13],"(pK(a)":[14],"values),":[15],"as":[16,54,61,118],"collated":[17],"from":[18],"the":[19,23,37,69,125,130,142],"primary":[20],"literature,":[21],"in":[22,36],"form":[24],"web-accessible":[27],"postgreSQL":[28],"relational":[29],"database.":[30],"Ionizable":[31],"residues":[32],"play":[33],"key":[34,115],"roles":[35],"molecular":[38],"mechanisms":[39],"that":[40,66],"underlie":[41],"many":[42],"biological":[43],"phenomena,":[44],"including":[45],"folding":[47],"and":[48,60,71,96,111,124],"enzyme":[49],"catalysis.":[50],"PPD":[52],"serves":[53],"general":[56],"archive":[59],"source":[63],"data":[65],"allows":[67],"for":[68,121],"development":[70],"improvement":[72],"prediction":[75],"systems.":[76],"database":[78,137],"is":[79],"accessed":[80],"through":[81],"an":[82,92],"HTML":[83],"interface,":[84],"which":[85],"offers":[86],"two":[87],"fast,":[88],"efficient":[89],"search":[90],"methods:":[91],"amino":[93],"acid-based":[94],"query":[95],"Basic":[98],"Local":[99],"Alignment":[100],"Search":[101],"Tool":[102],"search.":[103],"Entries":[104],"also":[105],"give":[106],"details":[107],"experimental":[109],"techniques":[110],"links":[112],"to":[113],"other":[114],"databases,":[116],"such":[117],"National":[119],"Center":[120],"Biotechnology":[122],"Information":[123],"Data":[127],"Bank,":[128],"providing":[129],"user":[131],"with":[132],"considerable":[133],"background":[134],"information.":[135],"can":[138],"be":[139],"found":[140],"at":[141],"following":[143],"URL:":[144],"http://www.jenner.ac.uk/PPD.":[145]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-01T08:36:08.643496","created_date":"2025-10-10T00:00:00"}
