{"id":"https://openalex.org/W2057601245","doi":"https://doi.org/10.1021/ci100332m","title":"Comments on the Article \u201cEvaluation of p<i>K</i><sub>a</sub> Estimation Methods on 211 Druglike Compounds\u201d","display_name":"Comments on the Article \u201cEvaluation of p<i>K</i><sub>a</sub> Estimation Methods on 211 Druglike Compounds\u201d","publication_year":2010,"publication_date":"2010-12-07","ids":{"openalex":"https://openalex.org/W2057601245","doi":"https://doi.org/10.1021/ci100332m","mag":"2057601245","pmid":"https://pubmed.ncbi.nlm.nih.gov/21138320"},"language":"en","primary_location":{"id":"doi:10.1021/ci100332m","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100332m","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"letter","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028715535","display_name":"John C. Shelley","orcid":"https://orcid.org/0000-0001-6223-4804"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John C. Shelley","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 101 SW Main Street, Portland, Oregon 97204, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 101 SW Main Street, Portland, Oregon 97204, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042631514","display_name":"David R. Calkins","orcid":null},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Calkins","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 101 SW Main Street, Portland, Oregon 97204, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 101 SW Main Street, Portland, Oregon 97204, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079162734","display_name":"Arron Sullivan","orcid":"https://orcid.org/0000-0003-4728-9713"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arron P. Sullivan","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 101 SW Main Street, Portland, Oregon 97204, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 101 SW Main Street, Portland, Oregon 97204, United States","institution_ids":["https://openalex.org/I203455613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5028715535"],"corresponding_institution_ids":["https://openalex.org/I203455613"],"apc_list":null,"apc_paid":null,"fwci":0.49598907,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.64600491,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"51","issue":"1","first_page":"102","last_page":"104"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13013","display_name":"Free Radicals and Antioxidants","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9991999864578247,"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/T12191","display_name":"Chemical Reaction Mechanisms","score":0.9957000017166138,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/mean-squared-error","display_name":"Mean squared error","score":0.7668753862380981},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.6791439652442932},{"id":"https://openalex.org/keywords/test-set","display_name":"Test set","score":0.5923882126808167},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5442843437194824},{"id":"https://openalex.org/keywords/estimation","display_name":"Estimation","score":0.5387495756149292},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.5222985744476318},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.5181351900100708},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5171146392822266},{"id":"https://openalex.org/keywords/work","display_name":"Work (physics)","score":0.4584396183490753},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.44826069474220276},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.36751389503479004},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3488275408744812},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3166061043739319},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2942468523979187},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24797001481056213}],"concepts":[{"id":"https://openalex.org/C139945424","wikidata":"https://www.wikidata.org/wiki/Q1940696","display_name":"Mean squared error","level":2,"score":0.7668753862380981},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6791439652442932},{"id":"https://openalex.org/C169903167","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Test set","level":2,"score":0.5923882126808167},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5442843437194824},{"id":"https://openalex.org/C96250715","wikidata":"https://www.wikidata.org/wiki/Q965330","display_name":"Estimation","level":2,"score":0.5387495756149292},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.5222985744476318},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.5181351900100708},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5171146392822266},{"id":"https://openalex.org/C18762648","wikidata":"https://www.wikidata.org/wiki/Q42213","display_name":"Work (physics)","level":2,"score":0.4584396183490753},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.44826069474220276},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.36751389503479004},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3488275408744812},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3166061043739319},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2942468523979187},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24797001481056213},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D055598","descriptor_name":"Chemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055598","descriptor_name":"Chemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055598","descriptor_name":"Chemical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048088","descriptor_name":"Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci100332m","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100332m","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:21138320","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21138320","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":3,"referenced_works":["https://openalex.org/W2027423337","https://openalex.org/W2042678771","https://openalex.org/W2047245810"],"related_works":["https://openalex.org/W2967771611","https://openalex.org/W2250140425","https://openalex.org/W2123376283","https://openalex.org/W3121237257","https://openalex.org/W1990237101","https://openalex.org/W4226059458","https://openalex.org/W2950583864","https://openalex.org/W1515802933","https://openalex.org/W3188543266","https://openalex.org/W1967596815"],"abstract_inverted_index":{"The":[0,105],"recent":[1],"article":[2],"\"Evaluation":[3],"of":[4,113,141,168],"pK(a)":[5,57],"Estimation":[6],"Methods":[7],"on":[8,170],"211":[9],"Druglike":[10],"Compounds\"":[11],"(":[12],"Manchester,":[13],"J.;":[14],"et":[15],"al.":[16],"J.":[17],"Chem":[18],"Inf.":[19],"Model.":[20],"2010,":[21],"50,":[22],"565-571":[23],")":[24],"reports":[25],"poor":[26,39],"results":[27],"for":[28,37,59,81,154],"the":[29,38,47,52,67,71,82,88,99,110,114,147,152,155,165],"program":[30],"Epik.":[31,104],"Here,":[32],"we":[33],"highlight":[34],"likely":[35],"sources":[36],"performance":[40,167],"and":[41,120],"describe":[42],"work":[43],"done":[44],"to":[45,55,65,79,158],"improve":[46,164],"performance.":[48],"Running":[49],"Epik":[50,121,148,169],"in":[51,98,129],"mode":[53],"intended":[54],"calculate":[56],"values":[58],"sequentially":[60],"adding/removing":[61],"protons,":[62],"as":[63],"needed":[64],"reproduce":[66],"experimental":[68],"conditions,":[69],"improves":[70,151],"root":[72],"mean":[73],"squared":[74],"error":[75],"(RMSE)":[76],"from":[77,87],"3.0":[78],"2.18":[80],"85":[83],"public":[84,111,156],"compounds":[85,157],"available":[86],"paper.":[89],"Despite":[90],"this":[91,130],"improvement,":[92],"there":[93],"are":[94,134],"still":[95],"other":[96],"programs":[97],"Manchester":[100],"paper":[101],"that":[102,109,133,139],"outperform":[103],"primary":[106],"reason":[107],"is":[108,117,122],"portion":[112],"data":[115,131],"set":[116,132,150],"not":[118],"diverse":[119],"missing":[123,143],"a":[124,171],"few":[125],"key":[126],"functional":[127,144],"groups":[128,145],"heavily":[135],"represented.":[136],"We":[137],"show":[138],"incorporation":[140],"these":[142,161],"into":[146],"training":[149],"RMSE":[153],"1.04.":[159],"Furthermore,":[160],"enhancements":[162],"help":[163],"overall":[166],"large":[172],"druglike":[173],"test":[174],"set.":[175]},"counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}