{"id":"https://openalex.org/W2046076062","doi":"https://doi.org/10.1021/ci400312v","title":"Molecular Recognition in a Diverse Set of Protein\u2013Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations","display_name":"Molecular Recognition in a Diverse Set of Protein\u2013Ligand Interactions Studied with Molecular Dynamics Simulations and End-Point Free Energy Calculations","publication_year":2013,"publication_date":"2013-09-15","ids":{"openalex":"https://openalex.org/W2046076062","doi":"https://doi.org/10.1021/ci400312v","mag":"2046076062","pmid":"https://pubmed.ncbi.nlm.nih.gov/24032517"},"language":"en","primary_location":{"id":"doi:10.1021/ci400312v","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci400312v","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/A5100408160","display_name":"Bo Wang","orcid":"https://orcid.org/0000-0002-9620-3413"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bo Wang","raw_affiliation_strings":["Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States","institution_ids":["https://openalex.org/I55769427","https://openalex.org/I4394709130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108122287","display_name":"Liwei Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liwei Li","raw_affiliation_strings":["Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States","institution_ids":["https://openalex.org/I55769427","https://openalex.org/I4394709130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031403355","display_name":"Thomas D. Hurley","orcid":"https://orcid.org/0000-0002-5942-1163"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas D. Hurley","raw_affiliation_strings":["Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States","institution_ids":["https://openalex.org/I55769427","https://openalex.org/I4394709130"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055133888","display_name":"Samy O. Meroueh","orcid":"https://orcid.org/0000-0002-3948-7499"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Samy O. Meroueh","raw_affiliation_strings":["Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana\rUniversity Department of Biochemistry and Molecular Biology, \u2021Center for Computational\rBiology and Bioinformatics, \u00a7Department of Chemistry and Chemical Biology (IUPUI), \u2225Stark Neurosciences\rResearch Institute, Indiana University School of Medicine, 535 Barnhill\rDrive, Indianapolis, Indiana 46202, United States","institution_ids":["https://openalex.org/I55769427","https://openalex.org/I4394709130"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5055133888"],"corresponding_institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"],"apc_list":null,"apc_paid":null,"fwci":5.8329,"has_fulltext":false,"cited_by_count":44,"citation_normalized_percentile":{"value":0.96411311,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"53","issue":"10","first_page":"2659","last_page":"2670"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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":0.9994999766349792,"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":0.9991000294685364,"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/isothermal-titration-calorimetry","display_name":"Isothermal titration calorimetry","score":0.7781170606613159},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6406990885734558},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5713126063346863},{"id":"https://openalex.org/keywords/conformational-entropy","display_name":"Conformational entropy","score":0.500770092010498},{"id":"https://openalex.org/keywords/electrostatics","display_name":"Electrostatics","score":0.4889005720615387},{"id":"https://openalex.org/keywords/entropy","display_name":"Entropy (arrow of time)","score":0.45557892322540283},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.43965452909469604},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.41269171237945557},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.34773221611976624},{"id":"https://openalex.org/keywords/physical-chemistry","display_name":"Physical chemistry","score":0.22138041257858276},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1588447093963623}],"concepts":[{"id":"https://openalex.org/C156911925","wikidata":"https://www.wikidata.org/wiki/Q643384","display_name":"Isothermal titration calorimetry","level":2,"score":0.7781170606613159},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6406990885734558},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5713126063346863},{"id":"https://openalex.org/C69308434","wikidata":"https://www.wikidata.org/wiki/Q5160266","display_name":"Conformational entropy","level":3,"score":0.500770092010498},{"id":"https://openalex.org/C117626034","wikidata":"https://www.wikidata.org/wiki/Q26336","display_name":"Electrostatics","level":2,"score":0.4889005720615387},{"id":"https://openalex.org/C106301342","wikidata":"https://www.wikidata.org/wiki/Q4117933","display_name":"Entropy (arrow of time)","level":2,"score":0.45557892322540283},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.43965452909469604},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.41269171237945557},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.34773221611976624},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.22138041257858276},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1588447093963623},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D002151","descriptor_name":"Calorimetry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002151","descriptor_name":"Calorimetry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002151","descriptor_name":"Calorimetry","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","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":"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":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000037","qualifier_name":"antagonists & inhibitors","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000819","qualifier_name":"agonists","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000819","qualifier_name":"agonists","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000819","qualifier_name":"agonists","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","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":5,"locations":[{"id":"doi:10.1021/ci400312v","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci400312v","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:24032517","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24032517","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:europepmc.org:3175041","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4058328","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:scholarworks.indianapolis.iu.edu:1805/6774","is_oa":false,"landing_page_url":"https://hdl.handle.net/1805/6774","pdf_url":null,"source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PMC","raw_type":"Article"},{"id":"pmh:oai:scholarworks.iupui.edu:1805/6774","is_oa":false,"landing_page_url":"http://hdl.handle.net/1805/6774","pdf_url":null,"source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PMC","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.9100000262260437,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2588474362","display_name":null,"funder_award_id":"R21 AA019746","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G2984736520","display_name":null,"funder_award_id":"CA135380","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3685900827","display_name":null,"funder_award_id":"R01 CA135380","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7994791568","display_name":null,"funder_award_id":"P41 RR006009","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G8817424970","display_name":null,"funder_award_id":"AA0197461","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"}],"funders":[{"id":"https://openalex.org/F4320337330","display_name":"National Institute on Alcohol Abuse and Alcoholism","ror":"https://ror.org/02jzrsm59"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1549357029","https://openalex.org/W1973060079","https://openalex.org/W1976499671","https://openalex.org/W1977157176","https://openalex.org/W1978330227","https://openalex.org/W1993335095","https://openalex.org/W2000613080","https://openalex.org/W2001722230","https://openalex.org/W2001816314","https://openalex.org/W2003356525","https://openalex.org/W2014967718","https://openalex.org/W2018954741","https://openalex.org/W2019574809","https://openalex.org/W2021534482","https://openalex.org/W2023856915","https://openalex.org/W2027482274","https://openalex.org/W2031153203","https://openalex.org/W2033350048","https://openalex.org/W2034655166","https://openalex.org/W2037535298","https://openalex.org/W2040630181","https://openalex.org/W2043347718","https://openalex.org/W2047730466","https://openalex.org/W2052264682","https://openalex.org/W2063831812","https://openalex.org/W2069123478","https://openalex.org/W2075369230","https://openalex.org/W2087359404","https://openalex.org/W2089456079","https://openalex.org/W2092443343","https://openalex.org/W2106140689","https://openalex.org/W2115339329","https://openalex.org/W2121723608","https://openalex.org/W2146205494","https://openalex.org/W2147067341","https://openalex.org/W2159010139","https://openalex.org/W2161139798","https://openalex.org/W2164270482","https://openalex.org/W2170971420","https://openalex.org/W2325937861"],"related_works":["https://openalex.org/W1603964645","https://openalex.org/W1513758743","https://openalex.org/W1977157176","https://openalex.org/W2735568732","https://openalex.org/W2063295693","https://openalex.org/W2088280158","https://openalex.org/W2089497916","https://openalex.org/W2086429702","https://openalex.org/W1975093320","https://openalex.org/W2046076062"],"abstract_inverted_index":{"End-point":[0],"free":[1,20,41,99,111,115,211,220,267,331],"energy":[2,21,42,100,112,116,221,241],"calculations":[3,43,95],"using":[4,56,206],"MM-GBSA":[5,86,91,118,317],"and":[6,71,87,92,175,253,318],"MM-PBSA":[7,88,94,132,149,299],"provide":[8],"a":[9,45,123,180,287,294],"detailed":[10],"understanding":[11],"of":[12,48,63,126,164,183,202,316],"molecular":[13],"recognition":[14],"in":[15,29,107,141,144,195,293,297],"protein-ligand":[16,27,284],"interactions.":[17],"The":[18,61,186],"binding":[19,73],"can":[22],"be":[23],"used":[24],"to":[25,52,84,129,172,191,210,217,308,328],"rank-order":[26],"structures":[28],"virtual":[30],"screening":[31],"for":[32,44,131,148,153,250,264],"compound":[33],"or":[34],"target":[35],"identification.":[36],"Here,":[37],"we":[38],"carry":[39],"out":[40],"diverse":[46],"set":[47],"11":[49],"proteins":[50],"bound":[51],"14":[53],"small":[54],"molecules":[55],"extensive":[57],"explicit-solvent":[58],"MD":[59,192,280],"simulations.":[60],"structure":[62],"these":[64],"complexes":[65,285],"was":[66],"previously":[67],"solved":[68],"by":[69,246,282],"crystallography":[70],"their":[72],"studied":[74],"with":[75,122,133,234,260,286,339],"isothermal":[76],"titration":[77],"calorimetry":[78],"(ITC)":[79],"data":[80,263],"enabling":[81],"direct":[82],"comparison":[83],"the":[85,97,105,109,162,168,173,184,203,218,223,228,235,239,261,265,298,313,322,329,333,340],"calculations.":[89,117],"Four":[90],"three":[93],"reproduced":[96],"ITC":[98,219,236,262,330,341],"within":[101],"1":[102],"kcal\u00b7mol(-1)":[103],"highlighting":[104],"challenges":[106],"reproducing":[108],"absolute":[110],"from":[113,304],"end-point":[114],"exhibited":[119],"better":[120,146,181,216],"rank-ordering":[121,147,197,272],"Spearman":[124],"\u03c1":[125,305,309],"0.68":[127],"compared":[128],"0.40":[130,307],"dielectric":[134],"constant":[135],"(\u03b5":[136,301],"=":[137,151,155,199,276,302,306,310],"1).":[138],"An":[139],"increase":[140],"\u03b5":[142,154,159],"resulted":[143,194,292],"significantly":[145,160,215],"(\u03c1":[150,198,275],"0.91":[152],"10),":[156],"but":[157,227,269,320],"larger":[158],"reduced":[161],"contributions":[163],"electrostatics,":[165],"suggesting":[166],"that":[167,213],"improvement":[169,296],"is":[170,242,257,273],"due":[171],"nonpolar":[174,314],"entropy":[176,205],"components,":[177,324],"rather":[178],"than":[179,222],"representation":[182],"electrostatics.":[185],"SVRKB":[187],"scoring":[188],"function":[189],"applied":[190],"snapshots":[193,281],"excellent":[196],"0.81).":[200],"Calculations":[201],"configurational":[204],"normal-mode":[207],"analysis":[208],"led":[209],"energies":[212],"correlated":[214],"MD-based":[224],"quasi-harmonic":[225],"approach,":[226],"computed":[229,334],"entropies":[230,335],"showed":[231,325],"no":[232],"correlation":[233,327],"entropy.":[237,342],"When":[238],"adaptation":[240],"taken":[243],"into":[244],"consideration":[245],"running":[247],"separate":[248],"simulations":[249],"complex,":[251],"apo,":[252],"ligand":[254],"(MM-PBSAADAPT),":[255],"there":[256],"less":[258],"agreement":[259],"individual":[266],"energies,":[268],"remarkably":[270],"good":[271],"observed":[274],"0.89).":[277],"Interestingly,":[278],"filtering":[279],"prescoring":[283],"machine":[288],"learning-based":[289],"approach":[290],"(SVMSP)":[291],"significant":[295],"results":[300],"1)":[303],"0.81.":[311],"Finally,":[312],"components":[315],"MM-PBSA,":[319],"not":[321,337],"electrostatic":[323],"strong":[326],"energy;":[332],"did":[336],"correlate":[338]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}