{"id":"https://openalex.org/W3006469265","doi":"https://doi.org/10.1007/s10822-020-00280-7","title":"Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states","display_name":"Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states","publication_year":2020,"publication_date":"2020-02-12","ids":{"openalex":"https://openalex.org/W3006469265","doi":"https://doi.org/10.1007/s10822-020-00280-7","mag":"3006469265","pmid":"https://pubmed.ncbi.nlm.nih.gov/32052350"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-020-00280-7","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-020-00280-7","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7556740","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034201179","display_name":"M. R. Gunner","orcid":"https://orcid.org/0000-0003-1120-5776"},"institutions":[{"id":"https://openalex.org/I125687163","display_name":"City College of New York","ror":"https://ror.org/00wmhkr98","country_code":"US","type":"education","lineage":["https://openalex.org/I125687163"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"M. R. Gunner","raw_affiliation_strings":["Department of Physics City College of New York, New York, NY, 10031, USA. mguner@ccny.cuny.edu","Department of Physics City College of New York, New York, NY, 10031, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics City College of New York, New York, NY, 10031, USA. mguner@ccny.cuny.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Physics City College of New York, New York, NY, 10031, USA","institution_ids":["https://openalex.org/I125687163"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102851762","display_name":"Taichi Murakami","orcid":"https://orcid.org/0009-0002-5193-2230"},"institutions":[{"id":"https://openalex.org/I125687163","display_name":"City College of New York","ror":"https://ror.org/00wmhkr98","country_code":"US","type":"education","lineage":["https://openalex.org/I125687163"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Taichi Murakami","raw_affiliation_strings":["Department of Physics City College of New York, New York, NY, 10031, USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics City College of New York, New York, NY, 10031, USA","institution_ids":["https://openalex.org/I125687163"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013124064","display_name":"Ari\u00ebn S. Rustenburg","orcid":"https://orcid.org/0000-0002-3422-0613"},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4210100942","display_name":"Tri-Institutional PhD Program in Chemical Biology","ror":"https://ror.org/016twdg30","country_code":"US","type":"education","lineage":["https://openalex.org/I4210100942"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ari\u00ebn S. Rustenburg","raw_affiliation_strings":["Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA","Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, 10065, USA","Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA"],"affiliations":[{"raw_affiliation_string":"Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Medical College, New York, NY, 10065, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA","institution_ids":["https://openalex.org/I4210100942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032042251","display_name":"Mehtap I\u015f\u0131k","orcid":"https://orcid.org/0000-0002-6789-952X"},"institutions":[{"id":"https://openalex.org/I4210100942","display_name":"Tri-Institutional PhD Program in Chemical Biology","ror":"https://ror.org/016twdg30","country_code":"US","type":"education","lineage":["https://openalex.org/I4210100942"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mehtap I\u015f\u0131k","raw_affiliation_strings":["Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA","Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, 10065, USA"],"affiliations":[{"raw_affiliation_string":"Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, 10065, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210100942"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083925073","display_name":"John D. Chodera","orcid":"https://orcid.org/0000-0003-0542-119X"},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John D. Chodera","raw_affiliation_strings":["Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA"],"affiliations":[{"raw_affiliation_string":"Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA","institution_ids":["https://openalex.org/I1334819555"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5034201179"],"corresponding_institution_ids":["https://openalex.org/I125687163"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":2.8684,"has_fulltext":false,"cited_by_count":31,"citation_normalized_percentile":{"value":0.91266908,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"34","issue":"5","first_page":"561","last_page":"573"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13013","display_name":"Free Radicals and Antioxidants","score":0.9998000264167786,"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":0.9998000264167786,"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/T12327","display_name":"Various Chemistry Research Topics","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical 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/T12191","display_name":"Chemical Reaction Mechanisms","score":0.9922000169754028,"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/tautomer","display_name":"Tautomer","score":0.8550591468811035},{"id":"https://openalex.org/keywords/protonation","display_name":"Protonation","score":0.7571568489074707},{"id":"https://openalex.org/keywords/ideal","display_name":"Ideal (ethics)","score":0.5652685165405273},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.5389270782470703},{"id":"https://openalex.org/keywords/state","display_name":"State (computer science)","score":0.4892394542694092},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4281911551952362},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3755049705505371},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.34730708599090576},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.25223851203918457},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.16505226492881775},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1490771770477295},{"id":"https://openalex.org/keywords/ion","display_name":"Ion","score":0.14737212657928467},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.07501208782196045},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.0728142261505127}],"concepts":[{"id":"https://openalex.org/C111233374","wikidata":"https://www.wikidata.org/wiki/Q334640","display_name":"Tautomer","level":2,"score":0.8550591468811035},{"id":"https://openalex.org/C30095370","wikidata":"https://www.wikidata.org/wiki/Q899488","display_name":"Protonation","level":3,"score":0.7571568489074707},{"id":"https://openalex.org/C2776639384","wikidata":"https://www.wikidata.org/wiki/Q840396","display_name":"Ideal (ethics)","level":2,"score":0.5652685165405273},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.5389270782470703},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.4892394542694092},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4281911551952362},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3755049705505371},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.34730708599090576},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.25223851203918457},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.16505226492881775},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1490771770477295},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.14737212657928467},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.07501208782196045},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0728142261505127},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"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":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":true},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1007/s10822-020-00280-7","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-020-00280-7","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:32052350","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32052350","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 computer-aided molecular design","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7556740","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7556740","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Comput Aided Mol Des","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7556740","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7556740","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Comput Aided Mol Des","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.7900000214576721}],"awards":[{"id":"https://openalex.org/G1060914766","display_name":null,"funder_award_id":"R01GM124270","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1514215252","display_name":null,"funder_award_id":"P30 CA008748","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2717947948","display_name":null,"funder_award_id":"MCB-1519640","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4902158216","display_name":null,"funder_award_id":"P30CA008748","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1153842025","https://openalex.org/W1488022185","https://openalex.org/W1990724722","https://openalex.org/W1994414353","https://openalex.org/W2003312854","https://openalex.org/W2016909911","https://openalex.org/W2020289337","https://openalex.org/W2022694548","https://openalex.org/W2027423337","https://openalex.org/W2032427406","https://openalex.org/W2050226017","https://openalex.org/W2086455899","https://openalex.org/W2120715487","https://openalex.org/W2345728461","https://openalex.org/W2521473082","https://openalex.org/W2581193797","https://openalex.org/W2809429873","https://openalex.org/W2884534695","https://openalex.org/W2886213433","https://openalex.org/W2886715180","https://openalex.org/W2888135782","https://openalex.org/W2888293530","https://openalex.org/W2895361356","https://openalex.org/W2896864964","https://openalex.org/W2943360058","https://openalex.org/W3204582573","https://openalex.org/W4211079109","https://openalex.org/W4253191544"],"related_works":["https://openalex.org/W2251438165","https://openalex.org/W4297103231","https://openalex.org/W2006553579","https://openalex.org/W2070940942","https://openalex.org/W2015887350","https://openalex.org/W2106027604","https://openalex.org/W2361129091","https://openalex.org/W2082158222","https://openalex.org/W4323359560","https://openalex.org/W2884165437"],"abstract_inverted_index":null,"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":4}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2020-02-24T00:00:00"}
