{"id":"https://openalex.org/W2565270315","doi":"https://doi.org/10.1021/acs.jcim.6b00373","title":"Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations","display_name":"Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations","publication_year":2016,"publication_date":"2016-12-20","ids":{"openalex":"https://openalex.org/W2565270315","doi":"https://doi.org/10.1021/acs.jcim.6b00373","mag":"2565270315","pmid":"https://pubmed.ncbi.nlm.nih.gov/27996253"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00373","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00373","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/A5058802779","display_name":"Ido Ben\u2010Shalom","orcid":"https://orcid.org/0000-0002-7237-1690"},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ido Y. Ben-Shalom","raw_affiliation_strings":["Institute\rfor Pharmaceutical and Medicinal Chemistry, Department of Mathematics\rand Natural Sciences, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute\rfor Pharmaceutical and Medicinal Chemistry, Department of Mathematics\rand Natural Sciences, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004652204","display_name":"Stefania Pfeiffer\u2010Marek","orcid":"https://orcid.org/0000-0003-2765-8155"},"institutions":[{"id":"https://openalex.org/I4210138838","display_name":"Sanofi (Germany)","ror":"https://ror.org/03ytdtb31","country_code":"DE","type":"company","lineage":["https://openalex.org/I3018075036","https://openalex.org/I4210138838"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stefania Pfeiffer-Marek","raw_affiliation_strings":["LGCR/Pharmaceutical\rSciences Operations, Sanofi-Aventis Deutschland GmbH, Industriepark H\u00f6chst, 65926 Frankfurt am Main, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LGCR/Pharmaceutical\rSciences Operations, Sanofi-Aventis Deutschland GmbH, Industriepark H\u00f6chst, 65926 Frankfurt am Main, Germany","institution_ids":["https://openalex.org/I4210138838"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038155615","display_name":"Karl\u2010Heinz Baringhaus","orcid":"https://orcid.org/0000-0002-8435-1101"},"institutions":[{"id":"https://openalex.org/I4210138838","display_name":"Sanofi (Germany)","ror":"https://ror.org/03ytdtb31","country_code":"DE","type":"company","lineage":["https://openalex.org/I3018075036","https://openalex.org/I4210138838"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Karl-Heinz Baringhaus","raw_affiliation_strings":["R&D Resources/Site Direction, Sanofi-Aventis Deutschland GmbH, Industriepark H\u00f6chst, 65926 Frankfurt am Main, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"R&D Resources/Site Direction, Sanofi-Aventis Deutschland GmbH, Industriepark H\u00f6chst, 65926 Frankfurt am Main, Germany","institution_ids":["https://openalex.org/I4210138838"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063949219","display_name":"Holger Gohlke","orcid":"https://orcid.org/0000-0001-8613-1447"},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Holger Gohlke","raw_affiliation_strings":["Institute\rfor Pharmaceutical and Medicinal Chemistry, Department of Mathematics\rand Natural Sciences, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8613-1447","affiliations":[{"raw_affiliation_string":"Institute\rfor Pharmaceutical and Medicinal Chemistry, Department of Mathematics\rand Natural Sciences, Heinrich Heine University D\u00fcsseldorf, 40225 D\u00fcsseldorf, Germany","institution_ids":["https://openalex.org/I44260953"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5058802779"],"corresponding_institution_ids":["https://openalex.org/I44260953"],"apc_list":null,"apc_paid":null,"fwci":6.1279,"has_fulltext":false,"cited_by_count":57,"citation_normalized_percentile":{"value":0.96568743,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"57","issue":"2","first_page":"170","last_page":"189"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9995999932289124,"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/T13539","display_name":"thermodynamics and calorimetric analyses","score":0.9973000288009644,"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/solvation","display_name":"Solvation","score":0.7018455862998962},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6207684278488159},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5688958168029785},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.539775550365448},{"id":"https://openalex.org/keywords/implicit-solvation","display_name":"Implicit solvation","score":0.5232038497924805},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.45674553513526917},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.42560315132141113},{"id":"https://openalex.org/keywords/binding-energy","display_name":"Binding energy","score":0.41177690029144287},{"id":"https://openalex.org/keywords/entropy","display_name":"Entropy (arrow of time)","score":0.4115332365036011},{"id":"https://openalex.org/keywords/root-mean-square","display_name":"Root mean square","score":0.41135403513908386},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.3777683973312378},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.3040810227394104},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2628200650215149},{"id":"https://openalex.org/keywords/atomic-physics","display_name":"Atomic physics","score":0.13921180367469788},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.12451016902923584}],"concepts":[{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.7018455862998962},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6207684278488159},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5688958168029785},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.539775550365448},{"id":"https://openalex.org/C64147673","wikidata":"https://www.wikidata.org/wiki/Q6007318","display_name":"Implicit solvation","level":4,"score":0.5232038497924805},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.45674553513526917},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.42560315132141113},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.41177690029144287},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.4115332365036011},{"id":"https://openalex.org/C71907059","wikidata":"https://www.wikidata.org/wiki/Q223323","display_name":"Root mean square","level":2,"score":0.41135403513908386},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.3777683973312378},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.3040810227394104},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2628200650215149},{"id":"https://openalex.org/C184779094","wikidata":"https://www.wikidata.org/wiki/Q26383","display_name":"Atomic physics","level":1,"score":0.13921180367469788},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.12451016902923584},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","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/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D012399","descriptor_name":"Rotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012399","descriptor_name":"Rotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012399","descriptor_name":"Rotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","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":"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.6b00373","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00373","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:27996253","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27996253","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":[{"display_name":"Affordable and clean energy","score":0.8700000047683716,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":167,"referenced_works":["https://openalex.org/W61914134","https://openalex.org/W265943136","https://openalex.org/W1408737002","https://openalex.org/W1502592231","https://openalex.org/W1507197149","https://openalex.org/W1525865910","https://openalex.org/W1526952765","https://openalex.org/W1565826566","https://openalex.org/W1566752206","https://openalex.org/W1572030366","https://openalex.org/W1575925050","https://openalex.org/W1925334442","https://openalex.org/W1965362429","https://openalex.org/W1966238197","https://openalex.org/W1968177278","https://openalex.org/W1969046853","https://openalex.org/W1969133212","https://openalex.org/W1969873373","https://openalex.org/W1972148009","https://openalex.org/W1974809008","https://openalex.org/W1975580333","https://openalex.org/W1976499671","https://openalex.org/W1984738107","https://openalex.org/W1985748743","https://openalex.org/W1986568494","https://openalex.org/W1987307888","https://openalex.org/W1989139698","https://openalex.org/W1990724722","https://openalex.org/W1994874881","https://openalex.org/W1998472423","https://openalex.org/W1999715990","https://openalex.org/W2001368737","https://openalex.org/W2003356525","https://openalex.org/W2003805073","https://openalex.org/W2005887227","https://openalex.org/W2008525757","https://openalex.org/W2011466399","https://openalex.org/W2011600249","https://openalex.org/W2015928143","https://openalex.org/W2017829285","https://openalex.org/W2021370489","https://openalex.org/W2022193415","https://openalex.org/W2026159488","https://openalex.org/W2028031397","https://openalex.org/W2029863180","https://openalex.org/W2033671450","https://openalex.org/W2035266068","https://openalex.org/W2035898950","https://openalex.org/W2037614800","https://openalex.org/W2038827564","https://openalex.org/W2038940556","https://openalex.org/W2039350725","https://openalex.org/W2042806682","https://openalex.org/W2045675519","https://openalex.org/W2046029732","https://openalex.org/W2047969388","https://openalex.org/W2048986518","https://openalex.org/W2051108246","https://openalex.org/W2051920745","https://openalex.org/W2052030759","https://openalex.org/W2053858804","https://openalex.org/W2058004635","https://openalex.org/W2059521474","https://openalex.org/W2061303388","https://openalex.org/W2061486876","https://openalex.org/W2066424433","https://openalex.org/W2066583787","https://openalex.org/W2067174909","https://openalex.org/W2068782086","https://openalex.org/W2070701334","https://openalex.org/W2070818058","https://openalex.org/W2072384813","https://openalex.org/W2073023478","https://openalex.org/W2073714240","https://openalex.org/W2075369230","https://openalex.org/W2083946713","https://openalex.org/W2085825696","https://openalex.org/W2086787471","https://openalex.org/W2087466582","https://openalex.org/W2087661061","https://openalex.org/W2089442765","https://openalex.org/W2089692302","https://openalex.org/W2090241673","https://openalex.org/W2091669469","https://openalex.org/W2092443343","https://openalex.org/W2094057648","https://openalex.org/W2094825303","https://openalex.org/W2095372567","https://openalex.org/W2095691435","https://openalex.org/W2095719702","https://openalex.org/W2096864392","https://openalex.org/W2096914244","https://openalex.org/W2097420030","https://openalex.org/W2097612485","https://openalex.org/W2098432123","https://openalex.org/W2098933757","https://openalex.org/W2098971704","https://openalex.org/W2099440534","https://openalex.org/W2100045416","https://openalex.org/W2100414180","https://openalex.org/W2100856184","https://openalex.org/W2101017457","https://openalex.org/W2103945336","https://openalex.org/W2104270610","https://openalex.org/W2105902442","https://openalex.org/W2106140689","https://openalex.org/W2107506448","https://openalex.org/W2108304234","https://openalex.org/W2108859370","https://openalex.org/W2112855704","https://openalex.org/W2113007147","https://openalex.org/W2114162221","https://openalex.org/W2114441129","https://openalex.org/W2114779636","https://openalex.org/W2116903488","https://openalex.org/W2117534886","https://openalex.org/W2118233996","https://openalex.org/W2118587156","https://openalex.org/W2123986806","https://openalex.org/W2124126888","https://openalex.org/W2125304058","https://openalex.org/W2127073449","https://openalex.org/W2128332459","https://openalex.org/W2128640429","https://openalex.org/W2129157803","https://openalex.org/W2129460449","https://openalex.org/W2130867670","https://openalex.org/W2131288855","https://openalex.org/W2138337932","https://openalex.org/W2139880162","https://openalex.org/W2142820798","https://openalex.org/W2142868265","https://openalex.org/W2144288821","https://openalex.org/W2144775933","https://openalex.org/W2145682943","https://openalex.org/W2147993766","https://openalex.org/W2149263899","https://openalex.org/W2155275960","https://openalex.org/W2157281740","https://openalex.org/W2158534713","https://openalex.org/W2158729922","https://openalex.org/W2158875201","https://openalex.org/W2159523138","https://openalex.org/W2165088901","https://openalex.org/W2165948287","https://openalex.org/W2166765429","https://openalex.org/W2169617040","https://openalex.org/W2171013059","https://openalex.org/W2175169368","https://openalex.org/W2204075485","https://openalex.org/W2235720733","https://openalex.org/W2238240583","https://openalex.org/W2265661434","https://openalex.org/W2323178299","https://openalex.org/W2325034207","https://openalex.org/W2329862012","https://openalex.org/W2397367200","https://openalex.org/W2404459885","https://openalex.org/W2582743722","https://openalex.org/W2949504121","https://openalex.org/W4234347480","https://openalex.org/W4235207874","https://openalex.org/W4243280602","https://openalex.org/W4246656072","https://openalex.org/W4252112222","https://openalex.org/W4253794406","https://openalex.org/W6632608449"],"related_works":["https://openalex.org/W1966793603","https://openalex.org/W2048341727","https://openalex.org/W2089507369","https://openalex.org/W2045242973","https://openalex.org/W1974433778","https://openalex.org/W2498829061","https://openalex.org/W4323037679","https://openalex.org/W2322826137","https://openalex.org/W2105465678","https://openalex.org/W2053689559"],"abstract_inverted_index":{"A":[0],"major":[1],"uncertainty":[2],"in":[3,25,41,63,68,91,95,103,177,206,321],"binding":[4,78,92,185,202,322,332],"free":[5,108,186,323],"energy":[6,149,324],"estimates":[7,258],"for":[8,171,292,318],"protein\u2013ligand":[9,77,153,165],"complexes":[10,166],"by":[11,114],"methods":[12,317],"such":[13],"as":[14],"MM-PB(GB)SA":[15],"or":[16,22,271],"docking":[17],"scores":[18],"results":[19,302],"from":[20,81],"neglecting":[21],"approximating":[23],"changes":[24,102,320],"the":[26,31,42,51,66,74,82,88,126,133,148,152,261,293,305],"configurational":[27],"entropies":[28,141],"(\u0394Sconfig.)":[29],"of":[30,53,65,73,132,147,151,164,167,191,263,330],"solutes.":[32],"In":[33],"MM/PB(GB)SA-type":[34],"calculations,":[35],"\u0394Sconfig.":[36,62,257],"has":[37],"usually":[38],"been":[39],"estimated":[40],"rigid":[43,266],"rotor,":[44,267],"harmonic":[45,268],"oscillator":[46,269],"approximation.":[47],"Here,":[48],"we":[49],"present":[50],"development":[52],"a":[54,189,276,282,308],"computationally":[55,310],"efficient":[56,312],"method":[57,89,279],"(termed":[58],"BEERT)":[59],"to":[60,111,157,175,200,246,287,314,333],"approximate":[61],"terms":[64],"reduction":[67],"translational":[69],"and":[70,106,116,135,196,254,297],"rotational":[71],"freedom":[72],"ligand":[75,120],"upon":[76],"(\u0394SR/T),":[79],"starting":[80],"flexible":[83],"molecule":[84],"approach.":[85],"We":[86],"test":[87],"successfully":[90],"affinity":[93],"computations":[94],"connection":[96],"with":[97,125,143,173,256],"MM-PBSA":[98,248,294],"effective":[99,249,295],"energies":[100,187,250,296],"describing":[101],"gas-phase":[104],"interactions":[105,124],"solvation":[107],"energies.":[109],"Compared":[110],"related":[112,179,328],"work":[113],"Ruvinsky":[115],"co-workers,":[117],"clustering":[118],"bound":[119],"poses":[121],"based":[122,259],"on":[123,260],"protein":[127],"rather":[128],"than":[129],"structural":[130],"similarity":[131],"poses,":[134],"an":[136,144],"appropriate":[137,289],"averaging":[138],"over":[139,188],"single":[140],"associated":[142],"individual":[145],"well":[146],"landscape":[150],"complex,":[154],"were":[155],"found":[156],"be":[158],"crucial.":[159],"Employing":[160],"three":[161,208],"data":[162,182,285],"sets":[163],"pharmacologically":[168],"relevant":[169],"targets":[170],"validation,":[172],"up":[174],"20,":[176],"part":[178],"ligands":[180,331],"per":[181],"set,":[183],"spanning":[184],"range":[190],"\u22647":[192],"kcal":[193,223,238],"mol\u20131,":[194],"reliable":[195],"predictive":[197],"linear":[198],"models":[199,241],"estimate":[201],"affinities":[203],"are":[204,242],"obtained":[205],"all":[207],"cases":[209],"(R2":[210],"=":[211,221,226,236],"0.54\u20130.72,":[212],"p":[213,228],"<":[214,229],"0.001,":[215],"root":[216,231],"mean":[217,232],"squared":[218,233],"error":[219,234],"S":[220],"0.78\u20131.44":[222],"mol\u20131;":[224],"q2":[225],"0.34\u20130.67,":[227],"0.05,":[230],"sPRESS":[235],"1.07\u20131.36":[237],"mol\u20131).":[239],"These":[240],"markedly":[243],"improved":[244],"compared":[245],"considering":[247],"alone,":[251],"scoring":[252],"functions,":[253],"combinations":[255],"number":[262],"rotatable":[264],"bonds,":[265],"approximation,":[270],"interaction":[272],"entropy":[273],"method.":[274],"As":[275],"limitation,":[277],"our":[278,301],"currently":[280],"requires":[281],"target-specific":[283],"training":[284],"set":[286],"identify":[288],"scaling":[290],"coefficients":[291],"BEERT":[298],"\u0394SR/T.":[299],"Still,":[300],"suggest":[303],"that":[304],"approach":[306],"is":[307],"valuable,":[309],"more":[311],"complement":[313],"existing":[315],"rigorous":[316],"estimating":[319],"across":[325],"structurally":[326],"(weakly)":[327],"series":[329],"one":[334],"target.":[335]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":9},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}