{"id":"https://openalex.org/W2020964197","doi":"https://doi.org/10.1007/s10822-013-9657-3","title":"Estimation of relative binding free energy based on a free energy variational principle for the FKBP-ligand system","display_name":"Estimation of relative binding free energy based on a free energy variational principle for the FKBP-ligand system","publication_year":2013,"publication_date":"2013-06-01","ids":{"openalex":"https://openalex.org/W2020964197","doi":"https://doi.org/10.1007/s10822-013-9657-3","mag":"2020964197","pmid":"https://pubmed.ncbi.nlm.nih.gov/23754464"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-013-9657-3","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-013-9657-3","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","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/A5089943725","display_name":"Takeshi Ashida","orcid":null},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Takeshi Ashida","raw_affiliation_strings":["Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan","Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu 525-8577, Shiga, Japan","institution_ids":[]},{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan","institution_ids":["https://openalex.org/I135768898"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103093592","display_name":"Takeshi Kikuchi","orcid":"https://orcid.org/0000-0002-0578-5965"},"institutions":[{"id":"https://openalex.org/I135768898","display_name":"Ritsumeikan University","ror":"https://ror.org/0197nmd03","country_code":"JP","type":"education","lineage":["https://openalex.org/I135768898","https://openalex.org/I4390039241"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takeshi Kikuchi","raw_affiliation_strings":["Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, 525-8577, Shiga, Japan","Ritsumeikan University"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, 525-8577, Shiga, Japan","institution_ids":["https://openalex.org/I135768898"]},{"raw_affiliation_string":"Ritsumeikan University","institution_ids":["https://openalex.org/I135768898"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5089943725"],"corresponding_institution_ids":["https://openalex.org/I135768898"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":0.149,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.56143044,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"27","issue":"6","first_page":"479","last_page":"490"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9941999912261963,"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":0.9941999912261963,"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/T12620","display_name":"Signaling Pathways in Disease","score":0.9854000210762024,"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/T11150","display_name":"Endoplasmic Reticulum Stress and Disease","score":0.9761000275611877,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/fkbp","display_name":"FKBP","score":0.690380334854126},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.6108559370040894},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.42609745264053345},{"id":"https://openalex.org/keywords/estimation","display_name":"Estimation","score":0.4174700081348419},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.35172173380851746},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33224189281463623},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3086872100830078},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3081880211830139},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.20269381999969482},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.16161981225013733},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.0994684100151062}],"concepts":[{"id":"https://openalex.org/C133956753","wikidata":"https://www.wikidata.org/wiki/Q583864","display_name":"FKBP","level":2,"score":0.690380334854126},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.6108559370040894},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.42609745264053345},{"id":"https://openalex.org/C96250715","wikidata":"https://www.wikidata.org/wiki/Q965330","display_name":"Estimation","level":2,"score":0.4174700081348419},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.35172173380851746},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33224189281463623},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3086872100830078},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3081880211830139},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.20269381999969482},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.16161981225013733},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0994684100151062},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","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}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022021","descriptor_name":"Tacrolimus Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022021","descriptor_name":"Tacrolimus Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022021","descriptor_name":"Tacrolimus Binding Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1007/s10822-013-9657-3","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-013-9657-3","pdf_url":null,"source":{"id":"https://openalex.org/S64621741","display_name":"Journal of Computer-Aided Molecular Design","issn_l":"0920-654X","issn":["0920-654X","1573-4951"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"pmid:23754464","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23754464","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 computer-aided molecular design","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8500000238418579}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W1523609263","https://openalex.org/W1573009101","https://openalex.org/W1579594936","https://openalex.org/W1625910593","https://openalex.org/W1971255156","https://openalex.org/W1972699938","https://openalex.org/W1975580333","https://openalex.org/W1975754427","https://openalex.org/W1976499671","https://openalex.org/W1982046519","https://openalex.org/W1984738107","https://openalex.org/W2004640547","https://openalex.org/W2006820723","https://openalex.org/W2018954741","https://openalex.org/W2023563495","https://openalex.org/W2024553805","https://openalex.org/W2026159488","https://openalex.org/W2036527573","https://openalex.org/W2037535298","https://openalex.org/W2040630181","https://openalex.org/W2044259546","https://openalex.org/W2048214699","https://openalex.org/W2054788798","https://openalex.org/W2064867387","https://openalex.org/W2065838297","https://openalex.org/W2067174909","https://openalex.org/W2067687494","https://openalex.org/W2070915333","https://openalex.org/W2083372216","https://openalex.org/W2085902776","https://openalex.org/W2088547439","https://openalex.org/W2089528283","https://openalex.org/W2092443343","https://openalex.org/W2096538948","https://openalex.org/W2106140689","https://openalex.org/W2110225266","https://openalex.org/W2112256151","https://openalex.org/W2116696124","https://openalex.org/W2122315752","https://openalex.org/W2122977308","https://openalex.org/W2131313124","https://openalex.org/W2134450923","https://openalex.org/W2135984457","https://openalex.org/W2139721558","https://openalex.org/W2144288821","https://openalex.org/W2147993766","https://openalex.org/W2156495637","https://openalex.org/W2311078281","https://openalex.org/W2746796224","https://openalex.org/W4238009417"],"related_works":["https://openalex.org/W2024445825","https://openalex.org/W1973001216","https://openalex.org/W2054988261","https://openalex.org/W2015266032","https://openalex.org/W1984188257","https://openalex.org/W1970734629","https://openalex.org/W2426627080","https://openalex.org/W2091871192","https://openalex.org/W4210756688","https://openalex.org/W4388299804"],"abstract_inverted_index":null,"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
