{"id":"https://openalex.org/W2003065881","doi":"https://doi.org/10.1186/1758-2946-3-s1-p21","title":"LigpKa \u2013 a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations","display_name":"LigpKa \u2013 a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations","publication_year":2011,"publication_date":"2011-04-19","ids":{"openalex":"https://openalex.org/W2003065881","doi":"https://doi.org/10.1186/1758-2946-3-s1-p21","mag":"2003065881"},"language":"en","primary_location":{"id":"doi:10.1186/1758-2946-3-s1-p21","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p21","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P21","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P21","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031073197","display_name":"Paul Czodrowski","orcid":"https://orcid.org/0000-0002-7390-8795"},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]},{"id":"https://openalex.org/I164928964","display_name":"Merck KGaA, Darmstadt (Germany)","ror":"https://ror.org/04b2dty93","country_code":"DE","type":"company","lineage":["https://openalex.org/I164928964"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"P Czodrowski","raw_affiliation_strings":["Merck KGaA, Frankfurter Stra\u00dfe 250, D-64293, Darmstadt, Germany","Philipps-University Marburg, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35032, Marburg, Germany","Philipps-University Marburg, Institute of Pharmaceutical Chemistry, Marburg, Germany","Merck KGaA, Darmstadt, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck KGaA, Frankfurter Stra\u00dfe 250, D-64293, Darmstadt, Germany","institution_ids":["https://openalex.org/I164928964"]},{"raw_affiliation_string":"Philipps-University Marburg, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35032, Marburg, Germany","institution_ids":["https://openalex.org/I161103922"]},{"raw_affiliation_string":"Philipps-University Marburg, Institute of Pharmaceutical Chemistry, Marburg, Germany","institution_ids":["https://openalex.org/I161103922"]},{"raw_affiliation_string":"Merck KGaA, Darmstadt, Germany","institution_ids":["https://openalex.org/I164928964"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5097664741","display_name":"CR S\u00f8ndergaard","orcid":null},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]},{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK","IE"],"is_corresponding":false,"raw_author_name":"CR S\u00f8ndergaard","raw_affiliation_strings":["Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark","School of Biomolecular and Biomedical Science, Conway Institute, UCD, Dublin 4, Ireland","Department of Chemistry, University of Copenhagen, Copenhagen, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"School of Biomolecular and Biomedical Science, Conway Institute, UCD, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]},{"raw_affiliation_string":"Department of Chemistry, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011585013","display_name":"Sebastian Dohm","orcid":null},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"S Dohm","raw_affiliation_strings":["Philipps-University Marburg, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35032, Marburg, Germany","Philipps-University Marburg Institute of Pharmaceutical Chemistry Marburg GERMANY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Philipps-University Marburg, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35032, Marburg, Germany","institution_ids":["https://openalex.org/I161103922"]},{"raw_affiliation_string":"Philipps-University Marburg Institute of Pharmaceutical Chemistry Marburg GERMANY","institution_ids":["https://openalex.org/I161103922"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005420915","display_name":"G. Klebe","orcid":"https://orcid.org/0000-0002-4913-390X"},"institutions":[{"id":"https://openalex.org/I161103922","display_name":"Philipps University of Marburg","ror":"https://ror.org/01rdrb571","country_code":"DE","type":"education","lineage":["https://openalex.org/I161103922"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"G Klebe","raw_affiliation_strings":["Philipps-University Marburg, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35032, Marburg, Germany","Philipps-University Marburg Institute of Pharmaceutical Chemistry Marburg GERMANY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Philipps-University Marburg, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35032, Marburg, Germany","institution_ids":["https://openalex.org/I161103922"]},{"raw_affiliation_string":"Philipps-University Marburg Institute of Pharmaceutical Chemistry Marburg GERMANY","institution_ids":["https://openalex.org/I161103922"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082362785","display_name":"Jens Erik Nielsen","orcid":"https://orcid.org/0000-0002-2831-7718"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"JE Nielsen","raw_affiliation_strings":["School of Biomolecular and Biomedical Science, Conway Institute, UCD, Dublin 4, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Biomolecular and Biomedical Science, Conway Institute, UCD, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5031073197"],"corresponding_institution_ids":["https://openalex.org/I161103922","https://openalex.org/I164928964"],"apc_list":{"value":2190,"currency":"USD","value_usd":2190},"apc_paid":{"value":2190,"currency":"USD","value_usd":2190},"fwci":0.0,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.05846092,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"3","issue":"S1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13013","display_name":"Free Radicals and Antioxidants","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T13013","display_name":"Free Radicals and Antioxidants","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9973999857902527,"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"}},{"id":"https://openalex.org/T13180","display_name":"Chemistry and Chemical Engineering","score":0.9890999794006348,"subfield":{"id":"https://openalex.org/subfields/2304","display_name":"Environmental Chemistry"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protonation","display_name":"Protonation","score":0.820614218711853},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.6848601698875427},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.6836490631103516},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.5535170435905457},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.47385719418525696},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46666306257247925},{"id":"https://openalex.org/keywords/small-molecule","display_name":"Small molecule","score":0.44275084137916565},{"id":"https://openalex.org/keywords/value","display_name":"Value (mathematics)","score":0.4395880699157715},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3985525369644165},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.37787356972694397},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.3395993709564209},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.17626261711120605},{"id":"https://openalex.org/keywords/ion","display_name":"Ion","score":0.12016087770462036},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.09446179866790771}],"concepts":[{"id":"https://openalex.org/C30095370","wikidata":"https://www.wikidata.org/wiki/Q899488","display_name":"Protonation","level":3,"score":0.820614218711853},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6848601698875427},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.6836490631103516},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.5535170435905457},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.47385719418525696},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46666306257247925},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.44275084137916565},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.4395880699157715},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3985525369644165},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.37787356972694397},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.3395993709564209},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.17626261711120605},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.12016087770462036},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.09446179866790771},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1758-2946-3-s1-p21","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p21","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P21","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:c8792e123a244b5ab6f0d698da241ebf","is_oa":true,"landing_page_url":"https://doaj.org/article/c8792e123a244b5ab6f0d698da241ebf","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 3, Iss Suppl 1, p P21 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2091956","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3083576","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1758-2946-3-s1-p21","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1758-2946-3-s1-p21","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/1758-2946-3-S1-P21","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2003065881.pdf","grobid_xml":"https://content.openalex.org/works/W2003065881.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W945805037","https://openalex.org/W2021989727","https://openalex.org/W2081371352","https://openalex.org/W2070272790","https://openalex.org/W2021444944","https://openalex.org/W4295253044","https://openalex.org/W3093694997","https://openalex.org/W4253195378","https://openalex.org/W2017996710","https://openalex.org/W2082411620"],"abstract_inverted_index":{"Electrostatic":[0],"forces":[1],"play":[2],"a":[3,70,113,118,124,132],"large":[4],"role":[5],"in":[6,41,57,142],"determining":[7],"the":[8,14,47,55,59,81,109],"strength":[9],"of":[10,16,28,49,75,83,117,126],"protein-ligand":[11,31,119],"interactions,":[12],"and":[13,54,87,105,130],"calculation":[15,116],"pKa":[17,36,52,77,89,115,128,139],"value":[18,140],"shifts":[19],"upon":[20],"ligand":[21,50,65],"binding":[22,32],"is":[23],"therefore":[24],"an":[25],"important":[26],"component":[27],"any":[29],"accurate":[30,137],"calculation.":[33],"However,":[34],"such":[35,102],"calculations":[37,141],"are":[38],"rarely":[39],"performed":[40],"virtual":[42,143],"screening":[43,144],"experiments":[44],"due":[45],"to":[46],"unavailability":[48],"solution":[51,88],"values":[53,78,90,129],"difficulty":[56],"generating":[58,108],"required":[60],"charge":[61],"distributions":[62],"for":[63,91,107,112],"each":[64],"protonation":[66,85],"state.":[67],"We":[68],"present":[69],"freely":[71],"available":[72],"web-based":[73],"database":[74,122],"small-molecule":[76,92],"that":[79,95],"automates":[80],"task":[82],"retrieving":[84],"states":[86],"ligands":[93],"so":[94],"these":[96],"can":[97],"be":[98],"used":[99],"with":[100],"tools":[101],"as":[103],"PRODRG":[104],"PDB2PQR":[106],"necessary":[110],"parameters":[111],"structure-based":[114],"complex.":[120],"The":[121],"contains":[123],"total":[125],"348":[127],"represents":[131],"significant":[133],"step":[134],"towards":[135],"performing":[136],"automated":[138],"experiments.":[145]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-25T09:21:30.201066","created_date":"2025-10-10T00:00:00"}
