{"id":"https://openalex.org/W1978393297","doi":"https://doi.org/10.1063/1.4826261","title":"Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects","display_name":"Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects","publication_year":2013,"publication_date":"2013-11-08","ids":{"openalex":"https://openalex.org/W1978393297","doi":"https://doi.org/10.1063/1.4826261","mag":"1978393297","pmid":"https://pubmed.ncbi.nlm.nih.gov/24320250","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3838431"},"language":"en","primary_location":{"id":"doi:10.1063/1.4826261","doi":"https://doi.org/10.1063/1.4826261","is_oa":true,"landing_page_url":"https://doi.org/10.1063/1.4826261","pdf_url":"https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/1.4826261/9528413/184103_1_online.pdf","source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/1.4826261/9528413/184103_1_online.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065846695","display_name":"Gabriel J. Rocklin","orcid":"https://orcid.org/0000-0003-2253-5631","observed_orcids":["https://orcid.org/0000-0003-2253-5631"]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gabriel J. Rocklin","raw_affiliation_strings":["University of California San Francisco 1 Department of Pharmaceutical Chemistry, , 1700 4th St., San Francisco, California 94143-2550, USA and Biophysics Graduate Program, , 1700 4th St., San Francisco, California 94143-2550, USA","Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA and Biophysics Graduate Program, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California San Francisco 1 Department of Pharmaceutical Chemistry, , 1700 4th St., San Francisco, California 94143-2550, USA and Biophysics Graduate Program, , 1700 4th St., San Francisco, California 94143-2550, USA","institution_ids":["https://openalex.org/I180670191"]},{"raw_affiliation_string":"Department of Pharmaceutical Chemistry, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA and Biophysics Graduate Program, University of California San Francisco, 1700 4th St., San Francisco, California 94143-2550, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007496868","display_name":"David L. Mobley","orcid":"https://orcid.org/0000-0002-1083-5533","observed_orcids":["https://orcid.org/0000-0002-1083-5533"]},"institutions":[{"id":"https://openalex.org/I192396691","display_name":"LSU New Orleans","ror":"https://ror.org/034mtvk83","country_code":"US","type":"education","lineage":["https://openalex.org/I192396691"]},{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David L. Mobley","raw_affiliation_strings":["University of California Irvine 2 Departments of Pharmaceutical Sciences and Chemistry, , 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, , 2000 Lakeshore Drive, New Orleans, Louisiana 70148, USA","University of New Orleans 2 Departments of Pharmaceutical Sciences and Chemistry, , 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, , 2000 Lakeshore Drive, New Orleans, Louisiana 70148, USA","Departments of Pharmaceutical Sciences and Chemistry, University of California Irvine, 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of California Irvine 2 Departments of Pharmaceutical Sciences and Chemistry, , 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, , 2000 Lakeshore Drive, New Orleans, Louisiana 70148, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"University of New Orleans 2 Departments of Pharmaceutical Sciences and Chemistry, , 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, , 2000 Lakeshore Drive, New Orleans, Louisiana 70148, USA","institution_ids":["https://openalex.org/I192396691"]},{"raw_affiliation_string":"Departments of Pharmaceutical Sciences and Chemistry, University of California Irvine, 147 Bison Modular, Building 515, Irvine, California 92697-0001, USA and Department of Chemistry, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148, USA","institution_ids":["https://openalex.org/I192396691","https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013305919","display_name":"Ken A. Dill","orcid":"https://orcid.org/0000-0002-2390-2002","observed_orcids":["https://orcid.org/0000-0002-2390-2002"]},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ken A. Dill","raw_affiliation_strings":["5252 Stony Brook University 3 Laufer Center for Physical and Quantitative Biology, , Stony Brook, New York 11794-0001, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"5252 Stony Brook University 3 Laufer Center for Physical and Quantitative Biology, , Stony Brook, New York 11794-0001, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005181934","display_name":"Philippe H. H\u00fcnenberger","orcid":"https://orcid.org/0000-0002-9420-7998","observed_orcids":["https://orcid.org/0000-0002-9420-7998"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4405253565","display_name":"Laboratory of Physical Chemistry","ror":"https://ror.org/00v171g37","country_code":"CH","type":"facility","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088","https://openalex.org/I4405253565"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Philippe H. H\u00fcnenberger","raw_affiliation_strings":["Swiss Federal Institute of Technology 4 Laboratory of Physical Chemistry, , ETH, 8093 Z\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Swiss Federal Institute of Technology 4 Laboratory of Physical Chemistry, , ETH, 8093 Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088","https://openalex.org/I4405253565"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":null,"fwci":3.8491,"has_fulltext":true,"cited_by_count":238,"citation_normalized_percentile":{"value":0.95118167,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":"139","issue":"18","first_page":"184103","last_page":"184103"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.42800000309944153,"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":0.42800000309944153,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.2215999960899353,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.17419999837875366,"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/protein-ligand-binding-free-energy","display_name":"protein-ligand binding free energy","score":0.9459999799728394},{"id":"https://openalex.org/keywords/finite-size-effects","display_name":"finite-size effects","score":0.8820000290870667},{"id":"https://openalex.org/keywords/electrostatics","display_name":"electrostatics","score":0.5630000233650208},{"id":"https://openalex.org/keywords/periodic-boundary-conditions","display_name":"periodic boundary conditions","score":0.7799999713897705},{"id":"https://openalex.org/keywords/non-periodic-boundary-conditions","display_name":"non-periodic boundary conditions","score":0.8090000152587891},{"id":"https://openalex.org/keywords/poisson-boltzmann-equation","display_name":"Poisson-Boltzmann equation","score":0.7710000276565552},{"id":"https://openalex.org/keywords/charged-solutes","display_name":"charged solutes","score":0.5619999766349792},{"id":"https://openalex.org/keywords/cytochrome-c-peroxidase","display_name":"cytochrome c peroxidase","score":0.9319999814033508},{"id":"https://openalex.org/keywords/counterions","display_name":"counterions","score":0.5979999899864197},{"id":"https://openalex.org/keywords/explicit-solvent-model","display_name":"explicit solvent","score":0.49300000071525574},{"id":"https://openalex.org/keywords/continuum-electrostatics","display_name":"continuum electrostatics","score":0.7829999923706055}],"concepts":[{"id":"https://openalex.org/C112675119","wikidata":"https://www.wikidata.org/wiki/Q2992284","display_name":"Periodic boundary conditions","level":3,"score":0.6699458360671997},{"id":"https://openalex.org/C117626034","wikidata":"https://www.wikidata.org/wiki/Q26336","display_name":"Electrostatics","level":2,"score":0.5688897371292114},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5428867340087891},{"id":"https://openalex.org/C2781204021","wikidata":"https://www.wikidata.org/wiki/Q6497091","display_name":"Lattice (music)","level":2,"score":0.49610957503318787},{"id":"https://openalex.org/C182310444","wikidata":"https://www.wikidata.org/wiki/Q1332643","display_name":"Boundary value problem","level":2,"score":0.4711930751800537},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.45987123250961304},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.4291543662548065},{"id":"https://openalex.org/C41999313","wikidata":"https://www.wikidata.org/wiki/Q489328","display_name":"Molecular physics","level":1,"score":0.4161053001880646},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3938935399055481},{"id":"https://openalex.org/C184779094","wikidata":"https://www.wikidata.org/wiki/Q26383","display_name":"Atomic physics","level":1,"score":0.33524924516677856},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.32860058546066284},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3271017074584961},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.22680002450942993},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.183018296957016},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","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":[{"descriptor_ui":"D003578","descriptor_name":"Cytochrome-c Peroxidase","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003578","descriptor_name":"Cytochrome-c Peroxidase","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003578","descriptor_name":"Cytochrome-c Peroxidase","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000201","qualifier_name":"enzymology","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":true},{"descriptor_ui":"D013844","descriptor_name":"Thiazoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055672","descriptor_name":"Static Electricity","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}],"locations_count":5,"locations":[{"id":"doi:10.1063/1.4826261","doi":"https://doi.org/10.1063/1.4826261","is_oa":true,"landing_page_url":"https://doi.org/10.1063/1.4826261","pdf_url":"https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/1.4826261/9528413/184103_1_online.pdf","source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:3198050","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3838431","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3838431","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3838431","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"J Chem Phys","raw_type":"Text"},{"id":"pmid:24320250","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24320250","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,"listed_in":[],"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":"The Journal of chemical physics","raw_type":"Journal Article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt9g26g1ws","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/9g26g1ws","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"The Journal of Chemical Physics, vol 139, iss 18","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1063/1.4826261","doi":"https://doi.org/10.1063/1.4826261","is_oa":true,"landing_page_url":"https://doi.org/10.1063/1.4826261","pdf_url":"https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/1.4826261/9528413/184103_1_online.pdf","source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G489965017","display_name":"Enhanced sampling methods for the calculation of relative free energies from molecular dynamics simulations","funder_award_id":"132739","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G516714305","display_name":"Testing and improving alchemical techniques for predicting protein-ligand binding","funder_award_id":"R15GM096257","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5230049084","display_name":"Louisiana EPSCoR Research Infrastructure Improvement","funder_award_id":"1003897","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5797411922","display_name":null,"funder_award_id":"1R15GM096257-01A1","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6633794072","display_name":"New approaches for the efficient and accurate representation of the solvent in atomistic simulations","funder_award_id":"138020","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G8329092922","display_name":null,"funder_award_id":"EPS-1003897","funder_id":"https://openalex.org/F4320309392","funder_display_name":"Louisiana Board of Regents"},{"id":"https://openalex.org/G8953848041","display_name":null,"funder_award_id":"R15 GM096257","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"},{"id":"https://openalex.org/F4320309392","display_name":"Louisiana Board of Regents","ror":"https://ror.org/00jv89z46"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1978393297.pdf","grobid_xml":"https://content.openalex.org/works/W1978393297.grobid-xml"},"referenced_works_count":158,"referenced_works":["https://openalex.org/W27727037","https://openalex.org/W1505088694","https://openalex.org/W1521867405","https://openalex.org/W1579053109","https://openalex.org/W1612521140","https://openalex.org/W1625910593","https://openalex.org/W1672666614","https://openalex.org/W1757317193","https://openalex.org/W1891268890","https://openalex.org/W1966078827","https://openalex.org/W1966867657","https://openalex.org/W1970973025","https://openalex.org/W1971255156","https://openalex.org/W1971317029","https://openalex.org/W1974179545","https://openalex.org/W1974724221","https://openalex.org/W1975546420","https://openalex.org/W1975769356","https://openalex.org/W1976499671","https://openalex.org/W1977083651","https://openalex.org/W1977886012","https://openalex.org/W1977902160","https://openalex.org/W1978084071","https://openalex.org/W1979590514","https://openalex.org/W1979628588","https://openalex.org/W1979837325","https://openalex.org/W1984738107","https://openalex.org/W1987025068","https://openalex.org/W1988064521","https://openalex.org/W1988609333","https://openalex.org/W1994737524","https://openalex.org/W1994778680","https://openalex.org/W1994825230","https://openalex.org/W1997932867","https://openalex.org/W1998486888","https://openalex.org/W2001303516","https://openalex.org/W2001368885","https://openalex.org/W2001676859","https://openalex.org/W2002386039","https://openalex.org/W2003734403","https://openalex.org/W2004145462","https://openalex.org/W2004452275","https://openalex.org/W2005046515","https://openalex.org/W2009987871","https://openalex.org/W2013352984","https://openalex.org/W2014623535","https://openalex.org/W2016811530","https://openalex.org/W2016856091","https://openalex.org/W2017316247","https://openalex.org/W2017473653","https://openalex.org/W2017829285","https://openalex.org/W2018189050","https://openalex.org/W2018334040","https://openalex.org/W2019134072","https://openalex.org/W2019536189","https://openalex.org/W2020518606","https://openalex.org/W2020966733","https://openalex.org/W2021417836","https://openalex.org/W2022072508","https://openalex.org/W2023592877","https://openalex.org/W2024762727","https://openalex.org/W2027154929","https://openalex.org/W2028214652","https://openalex.org/W2028263411","https://openalex.org/W2029582401","https://openalex.org/W2030407582","https://openalex.org/W2032853185","https://openalex.org/W2034031073","https://openalex.org/W2035432821","https://openalex.org/W2035672721","https://openalex.org/W2035687084","https://openalex.org/W2036903029","https://openalex.org/W2037652551","https://openalex.org/W2038418805","https://openalex.org/W2040521312","https://openalex.org/W2041134840","https://openalex.org/W2042589464","https://openalex.org/W2043429268","https://openalex.org/W2044055096","https://openalex.org/W2044507301","https://openalex.org/W2045740527","https://openalex.org/W2046932130","https://openalex.org/W2046947907","https://openalex.org/W2048106802","https://openalex.org/W2048524630","https://openalex.org/W2048669879","https://openalex.org/W2049644498","https://openalex.org/W2051338962","https://openalex.org/W2052996108","https://openalex.org/W2053858804","https://openalex.org/W2054613133","https://openalex.org/W2058653824","https://openalex.org/W2059676982","https://openalex.org/W2060014271","https://openalex.org/W2061039629","https://openalex.org/W2065570049","https://openalex.org/W2066619150","https://openalex.org/W2067174909","https://openalex.org/W2067178485","https://openalex.org/W2068441201","https://openalex.org/W2072604508","https://openalex.org/W2073349483","https://openalex.org/W2073612372","https://openalex.org/W2073614606","https://openalex.org/W2078565255","https://openalex.org/W2080979642","https://openalex.org/W2081693079","https://openalex.org/W2082853624","https://openalex.org/W2083877845","https://openalex.org/W2088542750","https://openalex.org/W2090178047","https://openalex.org/W2093112373","https://openalex.org/W2093237456","https://openalex.org/W2097897594","https://openalex.org/W2102640727","https://openalex.org/W2102697248","https://openalex.org/W2103734924","https://openalex.org/W2104090745","https://openalex.org/W2104300835","https://openalex.org/W2107572441","https://openalex.org/W2110928212","https://openalex.org/W2112133710","https://openalex.org/W2113149246","https://openalex.org/W2114664060","https://openalex.org/W2118056979","https://openalex.org/W2127116852","https://openalex.org/W2127639535","https://openalex.org/W2128572087","https://openalex.org/W2129213941","https://openalex.org/W2132905138","https://openalex.org/W2140038584","https://openalex.org/W2140151763","https://openalex.org/W2141795095","https://openalex.org/W2143312174","https://openalex.org/W2144288821","https://openalex.org/W2144718643","https://openalex.org/W2146462263","https://openalex.org/W2153508513","https://openalex.org/W2155554859","https://openalex.org/W2155820514","https://openalex.org/W2155858732","https://openalex.org/W2156160283","https://openalex.org/W2156424691","https://openalex.org/W2159664507","https://openalex.org/W2160143001","https://openalex.org/W2163112106","https://openalex.org/W2168739509","https://openalex.org/W2322237199","https://openalex.org/W2323024366","https://openalex.org/W2324944408","https://openalex.org/W2333133288","https://openalex.org/W2475770862","https://openalex.org/W2600160877","https://openalex.org/W2963596279","https://openalex.org/W3023414588","https://openalex.org/W3149968680","https://openalex.org/W4247951394","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2313477640","https://openalex.org/W2156424691","https://openalex.org/W2899481329","https://openalex.org/W3000602429","https://openalex.org/W2790880845","https://openalex.org/W2899808977","https://openalex.org/W4410731881","https://openalex.org/W7172420052","https://openalex.org/W2110225266","https://openalex.org/W2049600900"],"abstract_inverted_index":{"The":[0,39,305],"calculation":[1],"of":[2,73,76,100,147,159,170,188,193,209,315,336,341,349,357,378],"a":[3,17,62,74,119,142,156,235,246,294,324,372],"protein-ligand":[4,257,393],"binding":[5,146],"free":[6,36,42,103,138,216,353],"energy":[7],"based":[8,244],"on":[9,16,107,135,212,245,255,299],"molecular":[10],"dynamics":[11],"(MD)":[12],"simulations":[13],"generally":[14],"relies":[15],"thermodynamic":[18],"cycle":[19],"in":[20,31,37,47,91,164,182,280,333,381,389],"which":[21,94],"the":[22,28,32,69,97,101,108,116,124,145,148,171,183,186,194,205,213,256,260,273,276,281,284,300,312,316,334,346,350,367,376],"ligand":[23,117,149],"is":[24,66,126,223,363],"alchemically":[25],"inserted":[26],"into":[27,311],"system,":[29,296],"both":[30,267],"solvated":[33],"protein":[34,125,172],"and":[35,56,111,191,237,249,269,400,407],"solution.":[38],"corresponding":[40],"ligand-insertion":[41],"energies":[43,139,217,354],"are":[44,105,228,243],"typically":[45],"calculated":[46,136],"nanoscale":[48],"computational":[49,196],"boxes":[50],"simulated":[51,79],"under":[52,80,266],"periodic":[53,63,270],"boundary":[54,82,271],"conditions":[55,83],"considering":[57],"electrostatic":[58,86],"interactions":[59],"defined":[60],"by":[61],"lattice-sum.":[64],"This":[65,88,130],"distinct":[67],"from":[68,200],"ideal":[70],"bulk":[71],"situation":[72],"system":[75],"macroscopic":[77],"size":[78,278,302,347],"non-periodic":[81,268,290],"with":[84],"Coulombic":[85],"interactions.":[87],"discrepancy":[89],"results":[90],"finite-size":[92,133,210,317,379],"effects,":[93,234],"affect":[95],"primarily":[96],"charging":[98,137,215,352],"component":[99],"insertion":[102],"energy,":[104],"dependent":[106],"box":[109,197,277,301,338],"size,":[110],"can":[112],"be":[113],"large":[114,207],"when":[115],"bears":[118],"net":[120],"charge,":[121],"especially":[122],"if":[123],"charged":[127,385],"as":[128,141,387],"well.":[129],"article":[131],"investigates":[132],"effects":[134,211,329,380],"using":[140],"test":[143],"case":[144],"2-amino-5-methylthiazole":[150],"(net":[151,173],"charge":[152,168],"+1":[153],"e)":[154],"to":[155,202,219,231,365,375],"mutant":[157],"form":[158],"yeast":[160],"cytochrome":[161],"c":[162],"peroxidase":[163],"water.":[165],"Considering":[166],"different":[167],"isoforms":[169],"charges":[174],"-5,":[175],"0,":[176],"+3,":[177],"or":[178,185],"+9":[179],"e),":[180],"either":[181,342],"absence":[184],"presence":[187],"neutralizing":[189],"counter-ions,":[190],"sizes":[192],"cubic":[195],"(edges":[198],"ranging":[199],"7.42":[201],"11.02":[203],"nm),":[204],"potentially":[206],"magnitude":[208],"raw":[214],"(up":[218],"17.1":[220],"kJ":[221,359],"mol(-1))":[222],"demonstrated.":[224],"Two":[225],"correction":[226,325,369],"schemes":[227,242,321],"then":[229],"proposed":[230],"eliminate":[232],"these":[233],"numerical":[236,261],"an":[238],"analytical":[239,285,368],"one.":[240],"Both":[241],"continuum-electrostatics":[247],"analysis":[248],"require":[250],"performing":[251],"Poisson-Boltzmann":[252],"(PB)":[253],"calculations":[254,265,292,383,390],"system.":[258],"While":[259],"scheme":[262,286,307,343,370],"requires":[263,288],"PB":[264,291],"conditions,":[272],"latter":[274,306],"at":[275],"considered":[279],"MD":[282],"simulations,":[283],"only":[287],"three":[289],"for":[293,326],"given":[295],"its":[297],"dependence":[298,348],"being":[303],"analytical.":[304],"also":[308,322],"provides":[309],"insight":[310],"physical":[313],"origin":[314],"effects.":[318],"These":[319],"two":[320],"encompass":[323],"discrete":[327],"solvent":[328],"that":[330],"persists":[331],"even":[332],"limit":[335],"infinite":[337],"sizes.":[339],"Application":[340],"essentially":[344],"eliminates":[345],"corrected":[351],"(maximal":[355],"deviation":[356],"1.5":[358],"mol(-1)).":[360],"Because":[361],"it":[362],"simple":[364],"apply,":[366],"offers":[371],"general":[373],"solution":[374],"problem":[377],"free-energy":[382],"involving":[384],"solutes,":[386],"encountered":[388],"concerning,":[391],"e.g.,":[392],"binding,":[394],"biomolecular":[395],"association,":[396],"residue":[397],"mutation,":[398],"pKa":[399],"redox":[401],"potential":[402],"estimation,":[403],"substrate":[404],"transformation,":[405],"solvation,":[406],"solvent-solvent":[408],"partitioning.":[409]},"counts_by_year":[{"year":2026,"cited_by_count":19},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":22},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":30},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":23},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":30},{"year":2017,"cited_by_count":21},{"year":2016,"cited_by_count":15},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":2}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2016-06-24T00:00:00"}