{"id":"https://openalex.org/W2947216665","doi":"https://doi.org/10.1021/acs.jcim.9b00363","title":"Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies","display_name":"Heterogeneous Dielectric Implicit Membrane Model for the Calculation of MMPBSA Binding Free Energies","publication_year":2019,"publication_date":"2019-05-30","ids":{"openalex":"https://openalex.org/W2947216665","doi":"https://doi.org/10.1021/acs.jcim.9b00363","mag":"2947216665","pmid":"https://pubmed.ncbi.nlm.nih.gov/31145610"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00363","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00363","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://www.ncbi.nlm.nih.gov/pmc/articles/7197397","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068949499","display_name":"D\u2019Artagnan Greene","orcid":"https://orcid.org/0000-0002-7836-9663"},"institutions":[{"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":"D\u2019Artagnan Greene","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012214235","display_name":"Ruxi Qi","orcid":"https://orcid.org/0000-0002-9243-1259"},"institutions":[{"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":"Ruxi Qi","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052669977","display_name":"Remy Nguyen","orcid":"https://orcid.org/0000-0002-2115-9059"},"institutions":[{"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":"Remy Nguyen","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034998760","display_name":"Tianyin Qiu","orcid":"https://orcid.org/0000-0002-3490-8469"},"institutions":[{"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":"Tianyin Qiu","raw_affiliation_strings":["Department of Chemistry, University of California, Irvine, California 92697, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, University of California, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032088629","display_name":"Ray Luo","orcid":"https://orcid.org/0000-0002-6346-8271"},"institutions":[{"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":true,"raw_author_name":"Ray Luo","raw_affiliation_strings":["Department of Molecular Biology and Biochemistry,\u00a0 Chemical and Materials Physics Graduate Program,\u00a0 Department of Biomedical Engineering,\u00a0 Department of Chemical and Biomolecular Engineering \u00a0and\u00a0 Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Biochemistry,\u00a0 Chemical and Materials Physics Graduate Program,\u00a0 Department of Biomedical Engineering,\u00a0 Department of Chemical and Biomolecular Engineering \u00a0and\u00a0 Department of Materials Science and Engineering, University of California, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5032088629"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":null,"apc_paid":null,"fwci":2.0612,"has_fulltext":false,"cited_by_count":47,"citation_normalized_percentile":{"value":0.87507696,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"59","issue":"6","first_page":"3041","last_page":"3056"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.998199999332428,"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":0.998199999332428,"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/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9957000017166138,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.9901999831199646,"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/membrane","display_name":"Membrane","score":0.5360458493232727},{"id":"https://openalex.org/keywords/dielectric","display_name":"Dielectric","score":0.5138257145881653},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.39645490050315857},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.3482576012611389},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3446500301361084},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.3297111988067627},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11933243274688721},{"id":"https://openalex.org/keywords/optoelectronics","display_name":"Optoelectronics","score":0.11395233869552612},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10832950472831726}],"concepts":[{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.5360458493232727},{"id":"https://openalex.org/C133386390","wikidata":"https://www.wikidata.org/wiki/Q184996","display_name":"Dielectric","level":2,"score":0.5138257145881653},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.39645490050315857},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3482576012611389},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3446500301361084},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.3297111988067627},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11933243274688721},{"id":"https://openalex.org/C49040817","wikidata":"https://www.wikidata.org/wiki/Q193091","display_name":"Optoelectronics","level":1,"score":0.11395233869552612},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10832950472831726}],"mesh":[{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"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":"D017097","descriptor_name":"Electric Impedance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017097","descriptor_name":"Electric Impedance","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017097","descriptor_name":"Electric Impedance","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},{"descriptor_ui":"D058470","descriptor_name":"Receptors, Purinergic P2Y","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058470","descriptor_name":"Receptors, Purinergic P2Y","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058470","descriptor_name":"Receptors, Purinergic P2Y","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058470","descriptor_name":"Receptors, Purinergic P2Y","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D058470","descriptor_name":"Receptors, Purinergic P2Y","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D058470","descriptor_name":"Receptors, Purinergic P2Y","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1021/acs.jcim.9b00363","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00363","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:31145610","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31145610","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:ark:/13030/qt3706p2n7","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt3706p2n7","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/3706p2n7","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,"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":"Journal of Chemical Information and Modeling, vol 59, iss 6","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7197397","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7197397","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 Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7197397","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7197397","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 Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[{"score":0.7799999713897705,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G1337535711","display_name":null,"funder_award_id":"GM093040","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8759326567","display_name":null,"funder_award_id":"GM079383","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":104,"referenced_works":["https://openalex.org/W98575952","https://openalex.org/W1493374012","https://openalex.org/W1553864921","https://openalex.org/W1606794504","https://openalex.org/W1964062494","https://openalex.org/W1966180932","https://openalex.org/W1966217539","https://openalex.org/W1968682237","https://openalex.org/W1968984443","https://openalex.org/W1973060079","https://openalex.org/W1973819621","https://openalex.org/W1975580333","https://openalex.org/W1978330227","https://openalex.org/W1978393297","https://openalex.org/W1984738107","https://openalex.org/W1987249971","https://openalex.org/W1990771438","https://openalex.org/W1994737524","https://openalex.org/W1995842153","https://openalex.org/W1999245179","https://openalex.org/W2000613080","https://openalex.org/W2004145462","https://openalex.org/W2005839003","https://openalex.org/W2012556902","https://openalex.org/W2018327545","https://openalex.org/W2018629314","https://openalex.org/W2023256284","https://openalex.org/W2028031397","https://openalex.org/W2028629022","https://openalex.org/W2030502598","https://openalex.org/W2031430636","https://openalex.org/W2035423970","https://openalex.org/W2035629195","https://openalex.org/W2036011280","https://openalex.org/W2036441926","https://openalex.org/W2036547515","https://openalex.org/W2039665613","https://openalex.org/W2048496209","https://openalex.org/W2048744137","https://openalex.org/W2053850750","https://openalex.org/W2054935927","https://openalex.org/W2055154757","https://openalex.org/W2056070858","https://openalex.org/W2060815747","https://openalex.org/W2061417691","https://openalex.org/W2063292547","https://openalex.org/W2063489644","https://openalex.org/W2064709968","https://openalex.org/W2066126934","https://openalex.org/W2066900663","https://openalex.org/W2068465600","https://openalex.org/W2070126787","https://openalex.org/W2072470496","https://openalex.org/W2073146967","https://openalex.org/W2073357661","https://openalex.org/W2074674539","https://openalex.org/W2083665636","https://openalex.org/W2088652291","https://openalex.org/W2089947617","https://openalex.org/W2090716237","https://openalex.org/W2091916224","https://openalex.org/W2092661111","https://openalex.org/W2093469889","https://openalex.org/W2095100698","https://openalex.org/W2095460759","https://openalex.org/W2096045964","https://openalex.org/W2106560147","https://openalex.org/W2106841278","https://openalex.org/W2107636991","https://openalex.org/W2110114082","https://openalex.org/W2110670340","https://openalex.org/W2112855704","https://openalex.org/W2114634948","https://openalex.org/W2118233996","https://openalex.org/W2130479394","https://openalex.org/W2132629607","https://openalex.org/W2134413226","https://openalex.org/W2140151763","https://openalex.org/W2142528678","https://openalex.org/W2142868265","https://openalex.org/W2145899756","https://openalex.org/W2155909615","https://openalex.org/W2157281740","https://openalex.org/W2162870748","https://openalex.org/W2169017143","https://openalex.org/W2323104785","https://openalex.org/W2331161041","https://openalex.org/W2346362410","https://openalex.org/W2407746632","https://openalex.org/W2417863416","https://openalex.org/W2509807444","https://openalex.org/W2515356632","https://openalex.org/W2555103584","https://openalex.org/W2583731463","https://openalex.org/W2598374030","https://openalex.org/W2604223107","https://openalex.org/W2606184670","https://openalex.org/W2609229915","https://openalex.org/W2768823327","https://openalex.org/W2783351753","https://openalex.org/W2899481329","https://openalex.org/W2900014623","https://openalex.org/W2904990417","https://openalex.org/W2915825875"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"Membrane-bound":[0],"protein":[1],"receptors":[2,110],"are":[3],"a":[4,40,133],"primary":[5],"biological":[6],"drug":[7,167],"target,":[8],"but":[9],"the":[10,63,81,89,98,107,127,142,154,160],"computational":[11],"analysis":[12],"of":[13,106,156,165],"membrane":[14,34,45,55,77,121,130,151],"proteins":[15],"has":[16,132],"been":[17],"limited.":[18],"In":[19],"order":[20],"to":[21,49,84,115,141],"improve":[22],"molecular":[23],"mechanics":[24],"Poisson-Boltzmann":[25],"surface":[26],"area":[27],"(MMPBSA)":[28],"binding":[29,94,138],"free":[30,50,95],"energy":[31,51],"calculations":[32,158],"for":[33,97,159],"protein-ligand":[35],"systems,":[36],"we":[37,124],"have":[38],"optimized":[39],"new":[41,68],"heterogeneous":[42,128],"dielectric":[43,75,82,129],"implicit":[44,76],"model,":[46],"with":[47,86,136],"respect":[48],"simulations":[52],"in":[53],"explicit":[54,57],"and":[56,59,104,112,123,163],"water,":[58],"implemented":[60],"it":[61],"into":[62],"Amber":[64],"software":[65],"suite.":[66],"This":[67,149],"model":[69,78,131,144,152],"supersedes":[70],"our":[71],"previous":[72],"uniform,":[73],"single":[74],"by":[79],"allowing":[80],"constant":[83],"vary":[85],"depth":[87],"within":[88],"membrane.":[90],"We":[91],"calculated":[92],"MMPBSA":[93,157],"energies":[96],"human":[99],"purinergic":[100],"platelet":[101],"receptor":[102],"(P2Y<sub>12</sub>R)":[103],"two":[105],"muscarinic":[108],"acetylcholine":[109],"(M2R":[111],"M3R)":[113],"bound":[114],"various":[116],"antagonist":[117],"ligands":[118],"using":[119],"both":[120],"models,":[122],"found":[125],"that":[126],"stronger":[134],"correlation":[135],"experimental":[137],"affinities":[139],"compared":[140],"older":[143],"under":[145],"otherwise":[146],"identical":[147],"conditions.":[148],"improved":[150],"increases":[153],"utility":[155],"rational":[161],"design":[162],"improvement":[164],"future":[166],"candidates.":[168]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}