{"id":"https://openalex.org/W3011377276","doi":"https://doi.org/10.1021/acs.jcim.0c00024","title":"Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein\u2013Ligand Binding Affinities","display_name":"Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein\u2013Ligand Binding Affinities","publication_year":2020,"publication_date":"2020-03-16","ids":{"openalex":"https://openalex.org/W3011377276","doi":"https://doi.org/10.1021/acs.jcim.0c00024","mag":"3011377276","pmid":"https://pubmed.ncbi.nlm.nih.gov/32175734"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00024","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00024","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035223959","display_name":"Ercheng Wang","orcid":"https://orcid.org/0000-0003-2074-4077"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ercheng Wang","raw_affiliation_strings":["Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061120915","display_name":"Hui Liu","orcid":"https://orcid.org/0000-0002-1267-2475"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Liu","raw_affiliation_strings":["Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100643054","display_name":"Junmei Wang","orcid":"https://orcid.org/0000-0002-9607-8229"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junmei Wang","raw_affiliation_strings":["Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023457285","display_name":"Gaoqi Weng","orcid":"https://orcid.org/0000-0001-8476-7548"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gaoqi Weng","raw_affiliation_strings":["Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011434518","display_name":"Huiyong Sun","orcid":"https://orcid.org/0000-0002-7107-7481"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huiyong Sun","raw_affiliation_strings":["Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100407681","display_name":"Zhe Wang","orcid":"https://orcid.org/0000-0003-4102-1353"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhe Wang","raw_affiliation_strings":["Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100624617","display_name":"Yu Kang","orcid":"https://orcid.org/0000-0002-0999-8802"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Kang","raw_affiliation_strings":["Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028525523","display_name":"Tingjun Hou","orcid":"https://orcid.org/0000-0001-7227-2580"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tingjun Hou","raw_affiliation_strings":["Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China"],"affiliations":[{"raw_affiliation_string":"Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China","institution_ids":["https://openalex.org/I76130692"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5028525523"],"corresponding_institution_ids":["https://openalex.org/I76130692"],"apc_list":null,"apc_paid":null,"fwci":3.006,"has_fulltext":false,"cited_by_count":55,"citation_normalized_percentile":{"value":0.93109458,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"60","issue":"11","first_page":"5353","last_page":"5365"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","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/T11124","display_name":"Protein purification and stability","score":0.9980999827384949,"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/dielectric","display_name":"Dielectric","score":0.6625545024871826},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5373111963272095},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4798692762851715},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.4705512821674347},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4495398998260498},{"id":"https://openalex.org/keywords/binding-affinities","display_name":"Binding affinities","score":0.43453675508499146},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.27978047728538513},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.22783911228179932},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.1366938054561615},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11309623718261719}],"concepts":[{"id":"https://openalex.org/C133386390","wikidata":"https://www.wikidata.org/wiki/Q184996","display_name":"Dielectric","level":2,"score":0.6625545024871826},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5373111963272095},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4798692762851715},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.4705512821674347},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4495398998260498},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.43453675508499146},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.27978047728538513},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.22783911228179932},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.1366938054561615},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11309623718261719},{"id":"https://openalex.org/C49040817","wikidata":"https://www.wikidata.org/wiki/Q193091","display_name":"Optoelectronics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":2,"locations":[{"id":"doi:10.1021/acs.jcim.0c00024","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00024","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:32175734","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32175734","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2260806423","display_name":null,"funder_award_id":"21575128","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5851892296","display_name":null,"funder_award_id":"LZ19H300001","funder_id":"https://openalex.org/F4320338464","funder_display_name":"Natural Science Foundation of Zhejiang Province"},{"id":"https://openalex.org/G7991011545","display_name":null,"funder_award_id":"81773632","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320338464","display_name":"Natural Science Foundation of Zhejiang Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":105,"referenced_works":["https://openalex.org/W137370206","https://openalex.org/W1212579592","https://openalex.org/W1549357029","https://openalex.org/W1968984443","https://openalex.org/W1969017960","https://openalex.org/W1969046853","https://openalex.org/W1973974137","https://openalex.org/W1975580333","https://openalex.org/W1976499671","https://openalex.org/W1977397081","https://openalex.org/W1978330227","https://openalex.org/W1981643696","https://openalex.org/W1997496427","https://openalex.org/W1997639796","https://openalex.org/W2004676220","https://openalex.org/W2006716188","https://openalex.org/W2011140003","https://openalex.org/W2013085020","https://openalex.org/W2017829285","https://openalex.org/W2018633278","https://openalex.org/W2019054779","https://openalex.org/W2019574809","https://openalex.org/W2024553805","https://openalex.org/W2025116694","https://openalex.org/W2030609780","https://openalex.org/W2031390939","https://openalex.org/W2035687084","https://openalex.org/W2037535298","https://openalex.org/W2037633994","https://openalex.org/W2039353947","https://openalex.org/W2039509403","https://openalex.org/W2041146739","https://openalex.org/W2043383571","https://openalex.org/W2046029732","https://openalex.org/W2047993019","https://openalex.org/W2048214699","https://openalex.org/W2051740084","https://openalex.org/W2054935927","https://openalex.org/W2065838297","https://openalex.org/W2066122522","https://openalex.org/W2066583787","https://openalex.org/W2067174909","https://openalex.org/W2069123478","https://openalex.org/W2075828031","https://openalex.org/W2079498967","https://openalex.org/W2084113057","https://openalex.org/W2084550263","https://openalex.org/W2085232512","https://openalex.org/W2088879148","https://openalex.org/W2089442765","https://openalex.org/W2094860818","https://openalex.org/W2094997513","https://openalex.org/W2095719702","https://openalex.org/W2095730783","https://openalex.org/W2098888753","https://openalex.org/W2100414180","https://openalex.org/W2105103540","https://openalex.org/W2105159282","https://openalex.org/W2106140689","https://openalex.org/W2109402847","https://openalex.org/W2116903488","https://openalex.org/W2117620409","https://openalex.org/W2120988271","https://openalex.org/W2122977308","https://openalex.org/W2128494768","https://openalex.org/W2129574204","https://openalex.org/W2131713387","https://openalex.org/W2134697181","https://openalex.org/W2139880162","https://openalex.org/W2140247386","https://openalex.org/W2140841928","https://openalex.org/W2142868265","https://openalex.org/W2146686098","https://openalex.org/W2146783323","https://openalex.org/W2147993766","https://openalex.org/W2148893085","https://openalex.org/W2151022427","https://openalex.org/W2151076845","https://openalex.org/W2152301091","https://openalex.org/W2171009743","https://openalex.org/W2191053675","https://openalex.org/W2331833821","https://openalex.org/W2470899874","https://openalex.org/W2516083692","https://openalex.org/W2554477349","https://openalex.org/W2558870009","https://openalex.org/W2578616381","https://openalex.org/W2618878549","https://openalex.org/W2742305903","https://openalex.org/W2766746980","https://openalex.org/W2769797696","https://openalex.org/W2783351753","https://openalex.org/W2796318934","https://openalex.org/W2803029512","https://openalex.org/W2808844862","https://openalex.org/W2889952976","https://openalex.org/W2891791233","https://openalex.org/W2892153093","https://openalex.org/W2893435209","https://openalex.org/W2900908302","https://openalex.org/W2904370362","https://openalex.org/W2951039542","https://openalex.org/W2954094311","https://openalex.org/W2968876990","https://openalex.org/W2995214848"],"related_works":["https://openalex.org/W3187200704","https://openalex.org/W2903287478","https://openalex.org/W2031259671","https://openalex.org/W3112966125","https://openalex.org/W1990832091","https://openalex.org/W4240532245","https://openalex.org/W1961356786","https://openalex.org/W4392059316","https://openalex.org/W2073233024","https://openalex.org/W1966443150"],"abstract_inverted_index":{"In":[0,54,77],"structure-based":[1],"drug":[2],"design":[3],"(SBDD),":[4],"the":[5,20,41,45,61,78,87,94,97,129,135,156,168,178,187,199,208,222,229,238,247],"molecular":[6],"mechanics":[7],"generalized":[8,47,69],"Born":[9,48,70],"surface":[10],"area":[11],"(MM/GBSA)":[12],"approach":[13,63],"has":[14],"been":[15],"widely":[16],"used":[17,51],"in":[18,52,197],"ranking":[19],"binding":[21,33,201,223],"affinity":[22,34],"of":[23,31,44,90,96,126,165,171,190,217],"small":[24],"molecule":[25],"ligands.":[26],"However,":[27],"an":[28,122],"accurate":[29],"estimation":[30],"protein-ligand":[32,173,183],"still":[35],"remains":[36],"a":[37,66,117,140,160,251],"challenge":[38],"due":[39],"to":[40,245],"intrinsic":[42],"limitation":[43],"standard":[46,157],"(GB)":[49],"model":[50,72,119],"MM/GBSA.":[53],"this":[55,104,193],"study,":[56],"we":[57,212],"proposed":[58],"and":[59,93,132],"evaluated":[60],"MM/GBSA":[62,114,158],"based":[64,115],"on":[65,116,177],"variable":[67],"dielectric":[68,75,82,98,124,142,163],"(VDGB)":[71],"using":[73],"residue-type-based":[74],"constants.":[76],"VDGB":[79,118],"model,":[80],"different":[81],"values":[83],"were":[84],"assigned":[85],"for":[86,100,128,134,144,167,204,254],"three":[88],"types":[89,102],"protein":[91,218],"residues,":[92],"magnitude":[95],"constants":[99],"residue":[101],"follows":[103],"order:":[105],"charged":[106,130],"\u2265":[107,109],"polar":[108],"nonpolar.":[110],"We":[111],"found":[112,213],"that":[113,214],"(MM/GBSA<sub>VDGB</sub>)":[120],"with":[121,139,159,181],"optimal":[123],"constant":[125,164],"4.0":[127,166],"residues":[131,137,219],"1.0":[133],"noncharged":[136],"together":[138],"net-charge-dependent":[141],"value":[143],"ligands":[145,206],"achieved":[146],"better":[147,188],"predictions":[148],"as":[149,250],"judged":[150],"by":[151],"Pearson's":[152],"correlation":[153],"coefficient":[154],"than":[155],"uniform":[161],"solute":[162],"training":[169],"set":[170,180],"130":[172],"complexes.":[174],"The":[175],"prediction":[176,239],"test":[179],"165":[182],"complexes":[184],"also":[185],"validated":[186],"performance":[189],"MM/GBSA<sub>VDGB</sub>.":[191],"Moreover,":[192],"method":[194],"exhibited":[195],"potential":[196],"predicting":[198],"relative":[200],"free":[202],"energies":[203],"multiple":[205],"against":[207],"same":[209],"target.":[210],"Furthermore,":[211],"rational":[215],"truncation":[216],"far":[220],"from":[221],"site":[224],"can":[225],"significantly":[226],"speed":[227],"up":[228],"MM/GBSA<sub>VDGB</sub>":[230,249],"calculations,":[231],"while":[232],"it":[233,242],"almost":[234],"does":[235],"not":[236],"influence":[237],"accuracy.":[240],"Therefore,":[241],"is":[243],"feasible":[244],"implement":[246],"system-truncated":[248],"scoring":[252],"function":[253],"SBDD.":[255]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":4}],"updated_date":"2026-03-24T08:02:53.985720","created_date":"2025-10-10T00:00:00"}
