{"id":"https://openalex.org/W2045593942","doi":"https://doi.org/10.1002/(sici)1096-987x(19960730)17:10<1229::aid-jcc4>3.0.co;2-q","title":"Calculation of amino acid pKaS in a protein from a continuum electrostatic model: Method and sensitivity analysis","display_name":"Calculation of amino acid pKaS in a protein from a continuum electrostatic model: Method and sensitivity analysis","publication_year":1996,"publication_date":"1996-07-30","ids":{"openalex":"https://openalex.org/W2045593942","doi":"https://doi.org/10.1002/(sici)1096-987x(19960730)17:10<1229::aid-jcc4>3.0.co;2-q","mag":"2045593942"},"language":"en","primary_location":{"id":"doi:10.1002/(sici)1096-987x(19960730)17:10<1229::aid-jcc4>3.0.co;2-q","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19960730)17:10<1229::aid-jcc4>3.0.co;2-q","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5073521864","display_name":"Paul Beroza","orcid":"https://orcid.org/0000-0002-9407-1648"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"P. Beroza","raw_affiliation_strings":["Department of Physics, University of California, San Diego, La Jolla, California 92093","Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037"],"affiliations":[{"raw_affiliation_string":"Department of Physics, University of California, San Diego, La Jolla, California 92093","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037","institution_ids":["https://openalex.org/I123431417"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059130848","display_name":"D. R. Fredkin","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. R. Fredkin","raw_affiliation_strings":["Department of Physics, University of California, San Diego, La Jolla, California 92093","Department of Physics, University of California-San Diego, La Jolla, California 92093"],"affiliations":[{"raw_affiliation_string":"Department of Physics, University of California, San Diego, La Jolla, California 92093","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Physics, University of California-San Diego, La Jolla, California 92093","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5073521864"],"corresponding_institution_ids":["https://openalex.org/I123431417","https://openalex.org/I36258959"],"apc_list":{"value":4840,"currency":"USD","value_usd":4840},"apc_paid":null,"fwci":2.0119,"has_fulltext":false,"cited_by_count":46,"citation_normalized_percentile":{"value":0.87035587,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"17","issue":"10","first_page":"1229","last_page":"1244"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9980000257492065,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9980000257492065,"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/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11129","display_name":"Photochemistry and Electron Transfer Studies","score":0.9919999837875366,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/acid-dissociation-constant","display_name":"Acid dissociation constant","score":0.7983859777450562},{"id":"https://openalex.org/keywords/solvent-models","display_name":"Solvent models","score":0.6236806511878967},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6070716381072998},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.5018339157104492},{"id":"https://openalex.org/keywords/poisson\u2013boltzmann-equation","display_name":"Poisson\u2013Boltzmann equation","score":0.49854040145874023},{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.4093487858772278},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.3284394145011902},{"id":"https://openalex.org/keywords/ion","display_name":"Ion","score":0.3202040493488312},{"id":"https://openalex.org/keywords/physical-chemistry","display_name":"Physical chemistry","score":0.21500608325004578},{"id":"https://openalex.org/keywords/aqueous-solution","display_name":"Aqueous solution","score":0.19882187247276306}],"concepts":[{"id":"https://openalex.org/C22163223","wikidata":"https://www.wikidata.org/wiki/Q325519","display_name":"Acid dissociation constant","level":3,"score":0.7983859777450562},{"id":"https://openalex.org/C2779455329","wikidata":"https://www.wikidata.org/wiki/Q22908915","display_name":"Solvent models","level":4,"score":0.6236806511878967},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6070716381072998},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.5018339157104492},{"id":"https://openalex.org/C109757611","wikidata":"https://www.wikidata.org/wiki/Q901009","display_name":"Poisson\u2013Boltzmann equation","level":3,"score":0.49854040145874023},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.4093487858772278},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.3284394145011902},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.3202040493488312},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.21500608325004578},{"id":"https://openalex.org/C184651966","wikidata":"https://www.wikidata.org/wiki/Q906356","display_name":"Aqueous solution","level":2,"score":0.19882187247276306},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1002/(sici)1096-987x(19960730)17:10<1229::aid-jcc4>3.0.co;2-q","is_oa":false,"landing_page_url":"https://doi.org/10.1002/(sici)1096-987x(19960730)17:10<1229::aid-jcc4>3.0.co;2-q","pdf_url":null,"source":{"id":"https://openalex.org/S21117631","display_name":"Journal of Computational Chemistry","issn_l":"0192-8651","issn":["0192-8651","1096-987X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Chemistry","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W1974433778","https://openalex.org/W2902391471","https://openalex.org/W4296251651","https://openalex.org/W4281748313","https://openalex.org/W2120347752","https://openalex.org/W4323037679","https://openalex.org/W2062824236","https://openalex.org/W2140047262","https://openalex.org/W2089507369","https://openalex.org/W2098607050"],"abstract_inverted_index":{"We":[0],"used":[1],"continuum":[2,121],"electrostatic":[3,32,122],"theory":[4],"to":[5,22,41,58,64,80,113,142],"calculate":[6,81],"pKas":[7,40,96,103,154],"of":[8,37,45,47,72,94,119,133,146],"amino":[9,38],"acids":[10],"in":[11,97,116],"protein.":[12],"A":[13],"Green's":[14],"function":[15],"formalism,":[16],"based":[17],"on":[18],"a":[19,27,48,77,91],"finite-difference":[20],"solution":[21],"the":[23,56,60,73,82,98,117,120,131,134,147,160],"Poisson\u2013Boltzmann":[24],"equation":[25],"for":[26,107,144,159],"unit":[28],"point":[29],"charge,":[30],"yields":[31],"potentials":[33],"that":[34,109,127,155],"allow":[35],"calculation":[36],"acid":[39],"an":[42,69],"estimated":[43],"accuracy":[44,132],"tenths":[46],"pKa":[49,125],"unit.":[50],"Improvements":[51],"over":[52],"previous":[53],"methods":[54],"include":[55],"ability":[57],"focus":[59],"finite":[61],"difference":[62],"grid":[63,67],"arbitrarily":[65],"small":[66],"spacing,":[68],"analytical":[70],"representation":[71],"molecular":[74],"surface,":[75],"and":[76,151],"novel":[78],"procedure":[79],"reaction":[83,100,161],"field":[84],"potential.":[85],"Using":[86],"this":[87],"method,":[88,136],"we":[89],"performed":[90],"sensitivity":[92],"analysis":[93],"calculated":[95,150],"photosynthetic":[99],"center.":[101,162],"Calculated":[102],"are":[104,110,128],"most":[105],"sensitive":[106],"residues":[108],"not":[111,139],"well-exposed":[112],"solvent.":[114],"Variations":[115],"parameters":[118],"model":[123],"cause":[124],"shifts":[126],"larger":[129],"than":[130],"numerical":[135],"but":[137],"probably":[138],"large":[140],"enough":[141],"account":[143],"some":[145],"discrepancies":[148],"between":[149],"experimentally":[152],"measured":[153],"have":[156],"been":[157],"reported":[158],"\u00a9":[163],"1996":[164],"by":[165],"John":[166],"Wiley":[167],"&":[168],"Sons,":[169],"Inc.":[170]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
