{"id":"https://openalex.org/W3180334504","doi":"https://doi.org/10.1093/bioinformatics/btab518","title":"pKPDB: a protein data bank extension database of pKa and pI theoretical values","display_name":"pKPDB: a protein data bank extension database of pKa and pI theoretical values","publication_year":2021,"publication_date":"2021-07-08","ids":{"openalex":"https://openalex.org/W3180334504","doi":"https://doi.org/10.1093/bioinformatics/btab518","mag":"3180334504","pmid":"https://pubmed.ncbi.nlm.nih.gov/34260689"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab518","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab518","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.osti.gov/biblio/1813871","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053995866","display_name":"Pedro B. P. S. Reis","orcid":"https://orcid.org/0000-0003-3563-6239"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]},{"id":"https://openalex.org/I67348948","display_name":"Bayer (Germany)","ror":"https://ror.org/04hmn8g73","country_code":"DE","type":"company","lineage":["https://openalex.org/I67348948"]}],"countries":["DE","PT"],"is_corresponding":false,"raw_author_name":"Pedro B P S Reis","raw_affiliation_strings":["Bayer AG, Research & Development, Pharmaceuticals. Machine Learning Research, 13353 Berlin, Germany","Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal"],"raw_orcid":"https://orcid.org/0000-0003-3563-6239","affiliations":[{"raw_affiliation_string":"Bayer AG, Research & Development, Pharmaceuticals. Machine Learning Research, 13353 Berlin, Germany","institution_ids":["https://openalex.org/I67348948"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044662284","display_name":"Djork-Arn\u00e9 Clevert","orcid":"https://orcid.org/0000-0003-4191-2156"},"institutions":[{"id":"https://openalex.org/I67348948","display_name":"Bayer (Germany)","ror":"https://ror.org/04hmn8g73","country_code":"DE","type":"company","lineage":["https://openalex.org/I67348948"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Djork-Arn\u00e9 Clevert","raw_affiliation_strings":["Bayer AG, Research & Development, Pharmaceuticals. Machine Learning Research, 13353 Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bayer AG, Research & Development, Pharmaceuticals. Machine Learning Research, 13353 Berlin, Germany","institution_ids":["https://openalex.org/I67348948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061806501","display_name":"Miguel Machuqueiro","orcid":"https://orcid.org/0000-0001-6923-8744"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Miguel Machuqueiro","raw_affiliation_strings":["Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal"],"raw_orcid":"https://orcid.org/0000-0001-6923-8744","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal","institution_ids":["https://openalex.org/I141596103"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5061806501"],"corresponding_institution_ids":["https://openalex.org/I141596103"],"apc_list":{"value":3478,"currency":"USD","value_usd":3478},"apc_paid":null,"fwci":0.8205,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.70309595,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":98},"biblio":{"volume":"38","issue":"1","first_page":"297","last_page":"298"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5442000031471252,"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":0.5442000031471252,"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":0.04919999837875366,"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":0.048900000751018524,"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/computer-science","display_name":"Computer science","score":0.6908746361732483},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank","score":0.6662096977233887},{"id":"https://openalex.org/keywords/extension","display_name":"Extension (predicate logic)","score":0.6557389497756958},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.6271182298660278},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5805599093437195},{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.5780490636825562},{"id":"https://openalex.org/keywords/complement","display_name":"Complement (music)","score":0.5747430324554443},{"id":"https://openalex.org/keywords/isoelectric-point","display_name":"Isoelectric point","score":0.5083336234092712},{"id":"https://openalex.org/keywords/poisson-distribution","display_name":"Poisson distribution","score":0.4742635488510132},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4334193170070648},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.42459768056869507},{"id":"https://openalex.org/keywords/pi","display_name":"Pi","score":0.4101182222366333},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33723530173301697},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.3040122389793396},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20570465922355652},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.20243176817893982},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.18016254901885986},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.16059628129005432},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.15507245063781738},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.127597838640213}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6908746361732483},{"id":"https://openalex.org/C119145174","wikidata":"https://www.wikidata.org/wiki/Q7251429","display_name":"Protein Data Bank","level":3,"score":0.6662096977233887},{"id":"https://openalex.org/C2778029271","wikidata":"https://www.wikidata.org/wiki/Q5421931","display_name":"Extension (predicate logic)","level":2,"score":0.6557389497756958},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.6271182298660278},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5805599093437195},{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.5780490636825562},{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.5747430324554443},{"id":"https://openalex.org/C96294017","wikidata":"https://www.wikidata.org/wiki/Q308708","display_name":"Isoelectric point","level":3,"score":0.5083336234092712},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.4742635488510132},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4334193170070648},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.42459768056869507},{"id":"https://openalex.org/C53009064","wikidata":"https://www.wikidata.org/wiki/Q167","display_name":"Pi","level":2,"score":0.4101182222366333},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33723530173301697},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.3040122389793396},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20570465922355652},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.20243176817893982},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.18016254901885986},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16059628129005432},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.15507245063781738},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.127597838640213},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C188082640","wikidata":"https://www.wikidata.org/wiki/Q1780899","display_name":"Complementation","level":4,"score":0.0},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":"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":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","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":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab518","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab518","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34260689","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34260689","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":"Journal Article"},{"id":"pmh:oai:osti.gov:1813871","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1813871","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},{"id":"pmh:oai:osti.gov:1837314","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1837314","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null}],"best_oa_location":{"id":"pmh:oai:osti.gov:1813871","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1813871","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G191648531","display_name":null,"funder_award_id":"UIDB/04046/2020","funder_id":"https://openalex.org/F4320337197","funder_display_name":"Nuclear Fuel Cycle and Supply Chain"},{"id":"https://openalex.org/G5905153873","display_name":null,"funder_award_id":"SFRH/BD/136226/2018","funder_id":"https://openalex.org/F4320337197","funder_display_name":"Nuclear Fuel Cycle and Supply Chain"},{"id":"https://openalex.org/G6419962023","display_name":null,"funder_award_id":"CEECIND/02300/2017","funder_id":"https://openalex.org/F4320337197","funder_display_name":"Nuclear Fuel Cycle and Supply Chain"},{"id":"https://openalex.org/G799797873","display_name":null,"funder_award_id":"UIDP/04046/2020","funder_id":"https://openalex.org/F4320337197","funder_display_name":"Nuclear Fuel Cycle and Supply Chain"}],"funders":[{"id":"https://openalex.org/F4320337197","display_name":"Nuclear Fuel Cycle and Supply Chain","ror":"https://ror.org/05tj7dm33"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1975189886","https://openalex.org/W2008708467","https://openalex.org/W2020289337","https://openalex.org/W2056728743","https://openalex.org/W2100908214","https://openalex.org/W2108453057","https://openalex.org/W2114850508","https://openalex.org/W2130042185","https://openalex.org/W2130479394","https://openalex.org/W2546159719","https://openalex.org/W2916884115","https://openalex.org/W2950954328","https://openalex.org/W3082580455","https://openalex.org/W3098935468","https://openalex.org/W3177828909","https://openalex.org/W4293003482","https://openalex.org/W6652574002"],"related_works":["https://openalex.org/W2020669016","https://openalex.org/W2088162897","https://openalex.org/W2090630809","https://openalex.org/W4387804157","https://openalex.org/W2106612397","https://openalex.org/W2518314460","https://openalex.org/W2401430279","https://openalex.org/W2119891507","https://openalex.org/W2089869950","https://openalex.org/W2589205199"],"abstract_inverted_index":{"SUMMARY:":[0],"pKa":[1,57,73,109],"values":[2,58,112,157],"of":[3,9,52,85,116],"ionizable":[4],"residues":[5,138],"and":[6,14,20,33,74,92,110,113,125,130,154],"isoelectric":[7,155],"points":[8],"proteins":[10],"provide":[11,133],"valuable":[12],"local":[13],"global":[15],"insights":[16],"about":[17],"their":[18,83],"structure":[19],"function.":[21],"These":[22],"properties":[23],"can":[24,78,131,158,181],"be":[25,96,159,182],"estimated":[26],"with":[27],"reasonably":[28],"good":[29],"accuracy":[30],"using":[31],"Poisson-Boltzmann":[32],"Monte":[34],"Carlo":[35],"calculations":[36],"at":[37,175,184,192],"a":[38,50,165],"considerable":[39],"computational":[40,126],"cost":[41],"(from":[42],"some":[43],"minutes":[44],"to":[45],"several":[46],"hours).":[47],"pKPDB":[48,178],"is":[49,103],"database":[51,120],"over":[53,60],"12":[54],"M":[55],"theoretical":[56],"calculated":[59],"120k":[61],"protein":[62],"structures":[63],"deposited":[64],"in":[65,142],"the":[66,114,123,171],"Protein":[67],"Data":[68],"Bank.":[69],"By":[70],"providing":[71],"precomputed":[72],"pI":[75,111],"values,":[76],"users":[77],"retrieve":[79],"results":[80],"instantaneously":[81],"for":[82],"protein(s)":[84],"interest":[86],"while":[87],"also":[88,132],"saving":[89],"countless":[90],"hours":[91],"resources":[93],"that":[94,139],"would":[95],"spent":[97],"on":[98],"repeated":[99],"calculations.":[100],"Furthermore,":[101],"there":[102],"an":[104],"ever-growing":[105],"imbalance":[106],"between":[107],"experimental":[108,124,143],"number":[115],"resolved":[117],"structures.":[118],"This":[119],"will":[121],"complement":[122],"data":[127,189],"already":[128],"available":[129,191],"crucial":[134],"information":[135],"regarding":[136],"buried":[137],"are":[140,190],"under-represented":[141],"measurements.":[144],"AVAILABILITY":[145],"AND":[146],"IMPLEMENTATION:":[147],"Gzipped":[148],"csv":[149],"files":[150],"containing":[151],"p":[152],"Ka":[153],"point":[156],"downloaded":[160],"from":[161],"https://pypka.org/pKPDB.":[162],"To":[163],"query":[164],"single":[166],"PDB":[167],"code":[168,180],"please":[169],"use":[170],"PypKa":[172],"free":[173],"server":[174],"https://pypka.org.":[176],"The":[177],"source":[179],"found":[183],"https://github.com/mms-fcul/pKPDB.":[185],"SUPPLEMENTARY":[186],"INFORMATION:":[187],"Supplementary":[188],"Bioinformatics":[193],"online.":[194]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2021-07-19T00:00:00"}
