{"id":"https://openalex.org/W2982700906","doi":"https://doi.org/10.1021/acs.jcim.9b00754","title":"GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: p <i>K</i> <sub>a</sub> Predictions with Single-pH Simulations","display_name":"GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: p <i>K</i> <sub>a</sub> Predictions with Single-pH Simulations","publication_year":2019,"publication_date":"2019-10-29","ids":{"openalex":"https://openalex.org/W2982700906","doi":"https://doi.org/10.1021/acs.jcim.9b00754","mag":"2982700906","pmid":"https://pubmed.ncbi.nlm.nih.gov/31661616"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00754","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00754","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":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://figshare.com/articles/journal_contribution/GPU-Accelerated_Implementation_of_Continuous_Constant_pH_Molecular_Dynamics_in_Amber_p_i_K_i_sub_a_sub_Predictions_with_Single-pH_Simulations/10306505","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006410195","display_name":"Robert C. Harris","orcid":"https://orcid.org/0000-0002-1130-6457"},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert C. Harris","raw_affiliation_strings":["Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States"],"raw_orcid":"https://orcid.org/0000-0002-1130-6457","affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States","institution_ids":["https://openalex.org/I126744593"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084434392","display_name":"Jana Shen","orcid":"https://orcid.org/0000-0002-3234-0769"},"institutions":[{"id":"https://openalex.org/I126744593","display_name":"University of Maryland, Baltimore","ror":"https://ror.org/04rq5mt64","country_code":"US","type":"education","lineage":["https://openalex.org/I126744593"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jana Shen","raw_affiliation_strings":["Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States"],"raw_orcid":"https://orcid.org/0000-0002-3234-0769","affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States","institution_ids":["https://openalex.org/I126744593"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5084434392"],"corresponding_institution_ids":["https://openalex.org/I126744593"],"apc_list":null,"apc_paid":null,"fwci":2.5813,"has_fulltext":false,"cited_by_count":63,"citation_normalized_percentile":{"value":0.90979473,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"59","issue":"11","first_page":"4821","last_page":"4832"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9986000061035156,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9958000183105469,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.7757238149642944},{"id":"https://openalex.org/keywords/protonation","display_name":"Protonation","score":0.739633321762085},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6780236959457397},{"id":"https://openalex.org/keywords/replica","display_name":"Replica","score":0.5422365069389343},{"id":"https://openalex.org/keywords/titration","display_name":"Titration","score":0.5009157657623291},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3817560374736786},{"id":"https://openalex.org/keywords/analytical-chemistry","display_name":"Analytical Chemistry (journal)","score":0.35915428400039673},{"id":"https://openalex.org/keywords/physical-chemistry","display_name":"Physical chemistry","score":0.3121486306190491},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.14640888571739197}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7757238149642944},{"id":"https://openalex.org/C30095370","wikidata":"https://www.wikidata.org/wiki/Q899488","display_name":"Protonation","level":3,"score":0.739633321762085},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6780236959457397},{"id":"https://openalex.org/C2775937380","wikidata":"https://www.wikidata.org/wiki/Q1232589","display_name":"Replica","level":2,"score":0.5422365069389343},{"id":"https://openalex.org/C184866935","wikidata":"https://www.wikidata.org/wiki/Q191010","display_name":"Titration","level":2,"score":0.5009157657623291},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3817560374736786},{"id":"https://openalex.org/C113196181","wikidata":"https://www.wikidata.org/wiki/Q485223","display_name":"Analytical Chemistry (journal)","level":2,"score":0.35915428400039673},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.3121486306190491},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.14640888571739197},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","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/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","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":"D006863","descriptor_name":"Hydrogen-Ion Concentration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","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":false},{"descriptor_ui":"D011522","descriptor_name":"Protons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.9b00754","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00754","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:31661616","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31661616","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},{"id":"pmh:oai:europepmc.org:5883567","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6934042","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/10306505","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/GPU-Accelerated_Implementation_of_Continuous_Constant_pH_Molecular_Dynamics_in_Amber_p_i_K_i_sub_a_sub_Predictions_with_Single-pH_Simulations/10306505","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:figshare.com:article/10306505","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/GPU-Accelerated_Implementation_of_Continuous_Constant_pH_Molecular_Dynamics_in_Amber_p_i_K_i_sub_a_sub_Predictions_with_Single-pH_Simulations/10306505","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Clean water and sanitation","score":0.5099999904632568,"id":"https://metadata.un.org/sdg/6"}],"awards":[{"id":"https://openalex.org/G1239632752","display_name":null,"funder_award_id":"CBET-143595","funder_id":"https://openalex.org/F4320337390","funder_display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems"},{"id":"https://openalex.org/G1240835344","display_name":null,"funder_award_id":"R01GM118772","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3161687143","display_name":null,"funder_award_id":"R01 GM098818","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337390","display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems","ror":"https://ror.org/0471zv972"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W116310202","https://openalex.org/W2003312854","https://openalex.org/W2004822259","https://openalex.org/W2005006118","https://openalex.org/W2008174310","https://openalex.org/W2027408247","https://openalex.org/W2029582401","https://openalex.org/W2032187756","https://openalex.org/W2032427406","https://openalex.org/W2046102151","https://openalex.org/W2050447276","https://openalex.org/W2056728743","https://openalex.org/W2074225530","https://openalex.org/W2089495268","https://openalex.org/W2089578934","https://openalex.org/W2093177260","https://openalex.org/W2102174621","https://openalex.org/W2106140689","https://openalex.org/W2107317356","https://openalex.org/W2114764346","https://openalex.org/W2118171500","https://openalex.org/W2118571345","https://openalex.org/W2121529961","https://openalex.org/W2132262459","https://openalex.org/W2137399565","https://openalex.org/W2158667963","https://openalex.org/W2163168043","https://openalex.org/W2164270482","https://openalex.org/W2166478478","https://openalex.org/W2167864783","https://openalex.org/W2168240189","https://openalex.org/W2190363753","https://openalex.org/W2283762586","https://openalex.org/W2327581403","https://openalex.org/W2329540625","https://openalex.org/W2330088875","https://openalex.org/W2331716848","https://openalex.org/W2404280981","https://openalex.org/W2411825743","https://openalex.org/W2472763914","https://openalex.org/W2477513509","https://openalex.org/W2529068577","https://openalex.org/W2604909312","https://openalex.org/W2758005129","https://openalex.org/W2766450836","https://openalex.org/W2766915382","https://openalex.org/W2767829222","https://openalex.org/W2788212154","https://openalex.org/W2810398033","https://openalex.org/W2890361239","https://openalex.org/W2933867250","https://openalex.org/W3022867981","https://openalex.org/W4244370844"],"related_works":["https://openalex.org/W3013979739","https://openalex.org/W2655578171","https://openalex.org/W2577913821","https://openalex.org/W2460131733","https://openalex.org/W2953070151","https://openalex.org/W4296976839","https://openalex.org/W2372946558","https://openalex.org/W945805037","https://openalex.org/W2870404282","https://openalex.org/W2483707580"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,43,45,78,81,101,191,219,250,255,265,273,288,292,297,316,319],"GPU":[3],"implementation":[4],"of":[5,26,36,47,84,89,97,115,134,176,249,264,296,321,335],"the":[6,15,23,27,34,37,69,98,151,164,173,177,186,211,214,236,244],"continuous":[7,71,307],"constant":[8],"pH":[9,110,198],"molecular":[10,29],"dynamics":[11,30],"(CpHMD)":[12],"based":[13],"on":[14,272,291],"most":[16],"recent":[17],"generalized":[18],"Born":[19],"implicit-solvent":[20],"model":[21],"in":[22,59,155,163,254,312],"pmemd":[24],"engine":[25],"Amber":[28],"package.":[31],"To":[32],"test":[33,68],"accuracy":[35,116],"tool":[38],"for":[39,54,150,243,318,344],"rapid":[40],"p":[41,76,99,189,217,314],"K":[42,77,100,190,218,315],"predictions,":[44],"series":[46],"2":[48,125,135,171,229,260],"ns":[49,126,261],"single-pH":[50,165,233,245,262],"simulations":[51,123,166,203,234,248,326],"were":[52,64,103,193],"performed":[53],"over":[55,283],"120":[56],"titratable":[57],"residues":[58,179],"10":[60],"benchmark":[61],"proteins":[62],"that":[63,210,305],"previously":[65],"used":[66,311],"to":[67,93,119,181,195,331],"various":[70],"CpHMD":[72,289,308],"methods.":[73],"The":[74,238],"calculated":[75],"\u2019s":[79,102,220],"showed":[80,209],"root-mean-square":[82],"deviation":[83],"0.80":[85],"and":[86,129,140,185,339],"correlation":[87],"coefficient":[88],"0.83":[90],"with":[91,105,124,201,204,223,327],"respect":[92],"experiment.":[94],"Also,":[95],"90%":[96],"converged":[104,169],"estimated":[106],"errors":[107],"below":[108],"0.1":[109],"units.":[111],"Surprisingly,":[112],"this":[113],"level":[114],"is":[117,221,241,282],"similar":[118],"our":[120],"previous":[121],"replica-exchange":[122,202,247],"per":[127],"replica":[128],"an":[130],"exchange":[131,206,225],"attempt":[132,207],"frequency":[133],"ps":[136,230],"\u20131":[137],"(Huang,":[138],"Harris,":[139],"Shen":[141],"J.":[142],"Chem.":[143],"Inf.":[144],"Model.":[145],"2018,":[146],"58,":[147],"1372\u20131383).":[148],"Interestingly,":[149],"linked":[152,178],"titration":[153],"sites":[154],"two":[156,215],"enzymes,":[157],"although":[158],"residue-specific":[159],"protonation":[160,174,328],"state":[161,329],"sampling":[162],"was":[167],"not":[168],"within":[170,196],"ns,":[172],"fraction":[175],"appeared":[180],"be":[182,310],"largely":[183],"converged,":[184],"experimental":[187],"macroscopic":[188,216],"values":[192],"reproduced":[194],"1":[197,270],"unit.":[199],"Comparison":[200],"different":[205],"frequencies":[208],"splitting":[212],"between":[213],"underestimated":[222],"frequent":[224],"attempts":[226],"such":[227],"as":[228],"\u20131,":[231],"while":[232],"overestimate":[235],"splitting.":[237],"same":[239],"trend":[240],"seen":[242],"vs":[246],"hydrogen-bonded":[251],"aspartyl":[252],"dyad":[253],"much":[256],"larger":[257],"protein.":[258],"A":[259],"simulation":[263],"400-residue":[266],"protein":[267],"takes":[268],"about":[269],"h":[271],"single":[274,293],"NVIDIA":[275],"GeForce":[276],"RTX":[277],"2080":[278],"graphics":[279],"card,":[280],"which":[281],"1000":[284],"times":[285],"faster":[286],"than":[287],"run":[290],"CPU":[294],"core":[295],"high-performance":[298],"computing":[299],"cluster":[300],"node.":[301],"Thus,":[302],"we":[303],"envision":[304],"GPU-accelerated":[306],"may":[309],"routine":[313],"predictions":[317],"variety":[320],"applications,":[322],"from":[323],"assisting":[324],"MD":[325],"assignment":[330],"offering":[332],"pH-dependent":[333],"corrections":[334],"binding":[336],"free":[337],"energies":[338],"identifying":[340],"reactive":[341],"hot":[342],"spots":[343],"covalent":[345],"drug":[346],"design.":[347]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":13}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2019-11-08T00:00:00"}