{"id":"https://openalex.org/W2068782086","doi":"https://doi.org/10.1021/ci100458f","title":"Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA","display_name":"Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA","publication_year":2011,"publication_date":"2011-03-18","ids":{"openalex":"https://openalex.org/W2068782086","doi":"https://doi.org/10.1021/ci100458f","mag":"2068782086","pmid":"https://pubmed.ncbi.nlm.nih.gov/21417269"},"language":"en","primary_location":{"id":"doi:10.1021/ci100458f","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100458f","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://lup.lub.lu.se/record/1883786","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006219866","display_name":"Samuel Genheden","orcid":"https://orcid.org/0000-0002-7624-7363"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Samuel Genheden","raw_affiliation_strings":["Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden","Department of Theoretical Chemistry, Lund University, Chemical Centre , P.O. Box 124, SE-221 00 Lund, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]},{"raw_affiliation_string":"Department of Theoretical Chemistry, Lund University, Chemical Centre , P.O. Box 124, SE-221 00 Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109291626","display_name":"Ingemar Nilsson","orcid":null},"institutions":[{"id":"https://openalex.org/I4210143795","display_name":"AstraZeneca (Sweden)","ror":"https://ror.org/04wwrrg31","country_code":"SE","type":"company","lineage":["https://openalex.org/I105036370","https://openalex.org/I4210143795"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Ingemar Nilsson","raw_affiliation_strings":["Medicinal Chemistry, AstraZeneca R&D, SE-431 83 M\u00f6lndal, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medicinal Chemistry, AstraZeneca R&D, SE-431 83 M\u00f6lndal, Sweden","institution_ids":["https://openalex.org/I4210143795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030625494","display_name":"Ulf Ryde","orcid":"https://orcid.org/0000-0001-7653-8489"},"institutions":[{"id":"https://openalex.org/I187531555","display_name":"Lund University","ror":"https://ror.org/012a77v79","country_code":"SE","type":"education","lineage":["https://openalex.org/I187531555"]}],"countries":["SE"],"is_corresponding":true,"raw_author_name":"Ulf Ryde","raw_affiliation_strings":["Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden","Department of Theoretical Chemistry, Lund University, Chemical Centre , P.O. Box 124, SE-221 00 Lund, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]},{"raw_affiliation_string":"Department of Theoretical Chemistry, Lund University, Chemical Centre , P.O. Box 124, SE-221 00 Lund, Sweden","institution_ids":["https://openalex.org/I187531555"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5030625494"],"corresponding_institution_ids":["https://openalex.org/I187531555"],"apc_list":null,"apc_paid":null,"fwci":3.4098,"has_fulltext":false,"cited_by_count":78,"citation_normalized_percentile":{"value":0.93186795,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"51","issue":"4","first_page":"947","last_page":"958"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9882000088691711,"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/T10798","display_name":"Crystallography and molecular interactions","score":0.9828000068664551,"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/molecular-mechanics","display_name":"Molecular mechanics","score":0.7707163095474243},{"id":"https://openalex.org/keywords/binding-affinities","display_name":"Binding affinities","score":0.7095761895179749},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.6752171516418457},{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.5957620143890381},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5845771431922913},{"id":"https://openalex.org/keywords/thermodynamic-integration","display_name":"Thermodynamic integration","score":0.5455564260482788},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4980769157409668},{"id":"https://openalex.org/keywords/indole-test","display_name":"Indole test","score":0.43266212940216064},{"id":"https://openalex.org/keywords/quantitative-structure\u2013activity-relationship","display_name":"Quantitative structure\u2013activity relationship","score":0.41522717475891113},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.398527592420578},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.33057209849357605},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.271940141916275},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.16162109375},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1272868514060974},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11032432317733765},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.09981915354728699},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.08747607469558716}],"concepts":[{"id":"https://openalex.org/C25057246","wikidata":"https://www.wikidata.org/wiki/Q1344441","display_name":"Molecular mechanics","level":3,"score":0.7707163095474243},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.7095761895179749},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.6752171516418457},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.5957620143890381},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5845771431922913},{"id":"https://openalex.org/C141780669","wikidata":"https://www.wikidata.org/wiki/Q7783161","display_name":"Thermodynamic integration","level":3,"score":0.5455564260482788},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4980769157409668},{"id":"https://openalex.org/C192527728","wikidata":"https://www.wikidata.org/wiki/Q1465700","display_name":"Indole test","level":2,"score":0.43266212940216064},{"id":"https://openalex.org/C164126121","wikidata":"https://www.wikidata.org/wiki/Q766383","display_name":"Quantitative structure\u2013activity relationship","level":2,"score":0.41522717475891113},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.398527592420578},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.33057209849357605},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.271940141916275},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.16162109375},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1272868514060974},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11032432317733765},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.09981915354728699},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.08747607469558716}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000577","descriptor_name":"Amides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000577","descriptor_name":"Amides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000577","descriptor_name":"Amides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000578","descriptor_name":"Amidines","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000578","descriptor_name":"Amidines","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000578","descriptor_name":"Amidines","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007211","descriptor_name":"Indoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007211","descriptor_name":"Indoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007211","descriptor_name":"Indoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","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":"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":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015842","descriptor_name":"Serine Proteinase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D015842","descriptor_name":"Serine Proteinase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D015842","descriptor_name":"Serine Proteinase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D015842","descriptor_name":"Serine Proteinase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015842","descriptor_name":"Serine Proteinase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015842","descriptor_name":"Serine Proteinase Inhibitors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015951","descriptor_name":"Factor Xa","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D065427","descriptor_name":"Factor Xa Inhibitors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D065427","descriptor_name":"Factor Xa Inhibitors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D065427","descriptor_name":"Factor Xa Inhibitors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci100458f","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100458f","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:21417269","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21417269","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:lup.lub.lu.se:51ecd43d-240a-469c-8805-b1ae62065e2e","is_oa":true,"landing_page_url":"https://lup.lub.lu.se/record/1883786","pdf_url":null,"source":{"id":"https://openalex.org/S4306400536","display_name":"Lund University Publications (Lund University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I187531555","host_organization_name":"Lund University","host_organization_lineage":["https://openalex.org/I187531555"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1549-960X","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:lup.lub.lu.se:51ecd43d-240a-469c-8805-b1ae62065e2e","is_oa":true,"landing_page_url":"https://lup.lub.lu.se/record/1883786","pdf_url":null,"source":{"id":"https://openalex.org/S4306400536","display_name":"Lund University Publications (Lund University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I187531555","host_organization_name":"Lund University","host_organization_lineage":["https://openalex.org/I187531555"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1549-960X","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.9100000262260437}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1505406698","https://openalex.org/W1573009101","https://openalex.org/W1592950931","https://openalex.org/W1970973025","https://openalex.org/W1975580333","https://openalex.org/W1976161355","https://openalex.org/W1976499671","https://openalex.org/W1978330227","https://openalex.org/W1980618423","https://openalex.org/W1980937780","https://openalex.org/W1984157110","https://openalex.org/W1984341697","https://openalex.org/W1984738107","https://openalex.org/W1985407614","https://openalex.org/W1988562891","https://openalex.org/W1991261587","https://openalex.org/W1995807192","https://openalex.org/W1997612995","https://openalex.org/W2004124673","https://openalex.org/W2004676220","https://openalex.org/W2005860720","https://openalex.org/W2008130105","https://openalex.org/W2013475903","https://openalex.org/W2021283535","https://openalex.org/W2034541623","https://openalex.org/W2035266068","https://openalex.org/W2038780351","https://openalex.org/W2039353947","https://openalex.org/W2039781258","https://openalex.org/W2048214699","https://openalex.org/W2055751542","https://openalex.org/W2059434282","https://openalex.org/W2060002448","https://openalex.org/W2064060593","https://openalex.org/W2067174909","https://openalex.org/W2070915333","https://openalex.org/W2073662804","https://openalex.org/W2078565449","https://openalex.org/W2099826583","https://openalex.org/W2101936319","https://openalex.org/W2102537419","https://openalex.org/W2106140689","https://openalex.org/W2117417713","https://openalex.org/W2122199548","https://openalex.org/W2139880162","https://openalex.org/W2142820798","https://openalex.org/W2147993766","https://openalex.org/W2149062767","https://openalex.org/W2157281740","https://openalex.org/W2158534713","https://openalex.org/W2164270482","https://openalex.org/W2165526004","https://openalex.org/W2165894367","https://openalex.org/W4245765453","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W3187200704","https://openalex.org/W2031259671","https://openalex.org/W3112966125","https://openalex.org/W2108080735","https://openalex.org/W1990832091","https://openalex.org/W2095596733","https://openalex.org/W4240532245","https://openalex.org/W1961356786","https://openalex.org/W1966443150","https://openalex.org/W2068782086"],"abstract_inverted_index":{"We":[0],"present":[1],"free":[2,24],"energy":[3],"estimates":[4],"of":[5,9,36,125,135],"nine":[6],"3-amidinobenzyl-1H-indole-2-carboxamide":[7],"inhibitors":[8,45],"factor":[10],"Xa.":[11],"Using":[12],"alchemical":[13],"thermodynamic":[14],"integration":[15,87],"(TI)":[16],"calculations,":[17],"we":[18,55,67,70,94,150],"estimate":[19],"the":[20,37,44,58,73,97,104,119,136,141],"difference":[21],"in":[22,48,160],"binding":[23,64],"energies":[25],"with":[26,103,109],"high":[27,80],"accuracy":[28,81],"and":[29,52,82,89],"precision,":[30,83],"except":[31],"for":[32,118],"mutations":[33,120],"involving":[34],"one":[35],"amidinobenzyl":[38],"rings.":[39],"Crystal":[40],"studies":[41],"show":[42,56,68],"that":[43,57,69,121,134,153],"may":[46],"bind":[47],"two":[49,59],"distinct":[50],"conformations,":[51],"using":[53,85],"TI,":[54],"conformations":[60],"give":[61],"a":[62,79,123,130,157],"similar":[63,132],"affinity.":[65],"Furthermore,":[66],"can":[71],"reduce":[72],"computational":[74],"demand,":[75],"while":[76],"still":[77],"retaining":[78],"by":[84],"fewer":[86],"points":[88],"shorter":[90],"protein-ligand":[91],"simulations.":[92],"Finally,":[93],"have":[95,151],"compared":[96],"TI":[98,137,154],"results":[99,117],"to":[100,133],"those":[101],"obtained":[102],"simpler":[105],"MM/GBSA":[106,114,142],"method":[107,138,143],"(molecular-mechanics":[108],"generalized":[110],"Born":[111],"surface-area":[112],"solvation).":[113],"gives":[115],"better":[116],"involve":[122],"change":[124],"net":[126],"charge,":[127],"but":[128],"if":[129],"precision":[131],"is":[139,144],"required,":[140],"actually":[145],"slightly":[146],"more":[147],"expensive.":[148],"Thus,":[149],"shown":[152],"could":[155],"be":[156],"valuable":[158],"tool":[159],"drug":[161],"design.":[162]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":9}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
