{"id":"https://openalex.org/W2401605849","doi":"https://doi.org/10.1021/acs.jcim.5b00012","title":"Improving the LIE Method for Binding Free Energy Calculations of Protein\u2013Ligand Complexes","display_name":"Improving the LIE Method for Binding Free Energy Calculations of Protein\u2013Ligand Complexes","publication_year":2015,"publication_date":"2015-07-16","ids":{"openalex":"https://openalex.org/W2401605849","doi":"https://doi.org/10.1021/acs.jcim.5b00012","mag":"2401605849","pmid":"https://pubmed.ncbi.nlm.nih.gov/26180998"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5b00012","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00012","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/A5061031541","display_name":"Williams E. Miranda","orcid":"https://orcid.org/0000-0002-2735-5392"},"institutions":[{"id":"https://openalex.org/I2656126","display_name":"University of Havana","ror":"https://ror.org/04204gr61","country_code":"CU","type":"education","lineage":["https://openalex.org/I2656126"]}],"countries":["CU"],"is_corresponding":true,"raw_author_name":"Williams E. Miranda","raw_affiliation_strings":["Computational\rBiology and Biomolecular Dynamics Laboratory, Center for Protein Studies,\rFaculty of Biology, University of Havana, Havana, Cuba"],"affiliations":[{"raw_affiliation_string":"Computational\rBiology and Biomolecular Dynamics Laboratory, Center for Protein Studies,\rFaculty of Biology, University of Havana, Havana, Cuba","institution_ids":["https://openalex.org/I2656126"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029235749","display_name":"Sergei Y. Noskov","orcid":"https://orcid.org/0000-0001-7769-335X"},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Sergei Yu. Noskov","raw_affiliation_strings":["Centre\rfor Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada"],"affiliations":[{"raw_affiliation_string":"Centre\rfor Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047852894","display_name":"Pedro A. Valiente","orcid":"https://orcid.org/0000-0002-4776-6017"},"institutions":[{"id":"https://openalex.org/I2656126","display_name":"University of Havana","ror":"https://ror.org/04204gr61","country_code":"CU","type":"education","lineage":["https://openalex.org/I2656126"]}],"countries":["CU"],"is_corresponding":false,"raw_author_name":"Pedro A. Valiente","raw_affiliation_strings":["Computational\rBiology and Biomolecular Dynamics Laboratory, Center for Protein Studies,\rFaculty of Biology, University of Havana, Havana, Cuba"],"affiliations":[{"raw_affiliation_string":"Computational\rBiology and Biomolecular Dynamics Laboratory, Center for Protein Studies,\rFaculty of Biology, University of Havana, Havana, Cuba","institution_ids":["https://openalex.org/I2656126"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5061031541"],"corresponding_institution_ids":["https://openalex.org/I2656126"],"apc_list":null,"apc_paid":null,"fwci":1.4587,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.82348255,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"55","issue":"9","first_page":"1867","last_page":"1877"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.996999979019165,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9958999752998352,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5925190448760986},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5915075540542603},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.4314113259315491},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.37671560049057007},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2501925528049469},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17065614461898804},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.14624550938606262},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.09339636564254761}],"concepts":[{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5925190448760986},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5915075540542603},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.4314113259315491},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.37671560049057007},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2501925528049469},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17065614461898804},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.14624550938606262},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.09339636564254761}],"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":"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"D056831","descriptor_name":"Coordination Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056831","descriptor_name":"Coordination Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D056831","descriptor_name":"Coordination Complexes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5b00012","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5b00012","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:26180998","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26180998","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":0.8799999952316284,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G212363224","display_name":null,"funder_award_id":"RGPIN-315019","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G897777939","display_name":null,"funder_award_id":"F/5198-1","funder_id":"https://openalex.org/F4320320919","funder_display_name":"International Foundation for Science"}],"funders":[{"id":"https://openalex.org/F4320319907","display_name":"Alberta Innovates - Technology Futures","ror":"https://ror.org/00ynafe15"},{"id":"https://openalex.org/F4320320919","display_name":"International Foundation for Science","ror":"https://ror.org/03pwwck46"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":78,"referenced_works":["https://openalex.org/W408236731","https://openalex.org/W1507197149","https://openalex.org/W1513436357","https://openalex.org/W1521867405","https://openalex.org/W1538457056","https://openalex.org/W1573009101","https://openalex.org/W1619122155","https://openalex.org/W1874130373","https://openalex.org/W1976499671","https://openalex.org/W1980169714","https://openalex.org/W1981368164","https://openalex.org/W1991380804","https://openalex.org/W1991736661","https://openalex.org/W1994114759","https://openalex.org/W1998501624","https://openalex.org/W2001565260","https://openalex.org/W2005822853","https://openalex.org/W2010193651","https://openalex.org/W2018367409","https://openalex.org/W2029815870","https://openalex.org/W2030488214","https://openalex.org/W2030724380","https://openalex.org/W2035140261","https://openalex.org/W2035266068","https://openalex.org/W2035687084","https://openalex.org/W2037535298","https://openalex.org/W2042452143","https://openalex.org/W2043429268","https://openalex.org/W2044656372","https://openalex.org/W2048833096","https://openalex.org/W2048986518","https://openalex.org/W2050774715","https://openalex.org/W2051381895","https://openalex.org/W2053759741","https://openalex.org/W2057186508","https://openalex.org/W2059890035","https://openalex.org/W2060952378","https://openalex.org/W2062781237","https://openalex.org/W2065948973","https://openalex.org/W2067174909","https://openalex.org/W2078083982","https://openalex.org/W2081693079","https://openalex.org/W2083372216","https://openalex.org/W2083663804","https://openalex.org/W2084220260","https://openalex.org/W2084550263","https://openalex.org/W2086326523","https://openalex.org/W2096538948","https://openalex.org/W2100416227","https://openalex.org/W2103945336","https://openalex.org/W2107060723","https://openalex.org/W2107572441","https://openalex.org/W2110225266","https://openalex.org/W2113082449","https://openalex.org/W2122644949","https://openalex.org/W2127073449","https://openalex.org/W2130367897","https://openalex.org/W2130479394","https://openalex.org/W2131643298","https://openalex.org/W2135148464","https://openalex.org/W2138015848","https://openalex.org/W2144288821","https://openalex.org/W2146783323","https://openalex.org/W2147058445","https://openalex.org/W2147993766","https://openalex.org/W2152997175","https://openalex.org/W2153604743","https://openalex.org/W2157553215","https://openalex.org/W2159367911","https://openalex.org/W2162559665","https://openalex.org/W2167577803","https://openalex.org/W2323178299","https://openalex.org/W2977579634","https://openalex.org/W4233155785","https://openalex.org/W4238009417","https://openalex.org/W4245700002","https://openalex.org/W4246043393","https://openalex.org/W4253355670"],"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":{"In":[0],"this":[1],"work,":[2],"we":[3],"introduced":[4,43],"an":[5],"improved":[6],"linear":[7,27],"interaction":[8,132],"energy":[9],"(LIE)":[10],"method":[11],"parameterization":[12],"for":[13,77,115],"computations":[14],"of":[15,81],"protein\u2013ligand":[16,63,82,118],"binding":[17,74,112],"free":[18,75,113],"energies.":[19],"The":[20,47],"protocol,":[21],"coined":[22],"LIE-D,":[23],"builds":[24],"on":[25],"the":[26,30,35,40,50,72,111,121,126],"relationship":[28],"between":[29,53],"empirical":[31],"coefficient":[32],"\u03b3":[33],"in":[34,44,62],"standard":[36],"LIE":[37],"scheme":[38],"and":[39,56,98,128],"D":[41],"parameter,":[42],"our":[45,78],"work.":[46],"D-parameter":[48],"encompasses":[49],"balance":[51],"(difference)":[52],"electrostatic":[54,127],"(polar)":[55],"van":[57,129],"der":[58,130],"Waals":[59,131],"(nonpolar)":[60],"energies":[61,76,114,133],"complexes.":[64],"Leave-one-out":[65],"cross-validation":[66],"showed":[67],"that":[68],"LIE-D":[69,106],"reproduced":[70],"accurately":[71,110],"absolute":[73],"training":[79,122],"set":[80],"complexes":[83],"(<|error|>":[84],"=":[85,89,93,96,100],"0.92":[86],"kcal/mol,":[87,91],"SDerror":[88],"0.66":[90],"R(2)":[92],"0.90,":[94],"QLOO(2)":[95],"0.89,":[97],"sPRESS(LOO)":[99],"1.28":[101],"kcal/mol).":[102],"We":[103],"also":[104],"demonstrated":[105],"robustness":[107],"by":[108],"predicting":[109],"three":[116],"different":[117,137],"systems":[119],"outside":[120],"data":[123],"set,":[124],"where":[125],"were":[134],"calculated":[135],"with":[136],"force":[138],"fields.":[139]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
