{"id":"https://openalex.org/W1964048052","doi":"https://doi.org/10.1007/s10822-011-9525-y","title":"Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations","display_name":"Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations","publication_year":2011,"publication_date":"2011-12-23","ids":{"openalex":"https://openalex.org/W1964048052","doi":"https://doi.org/10.1007/s10822-011-9525-y","mag":"1964048052","pmid":"https://pubmed.ncbi.nlm.nih.gov/22198474"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-011-9525-y","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-011-9525-y","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3584352","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027168981","display_name":"Gerhard K\u00f6nig","orcid":"https://orcid.org/0000-0003-4898-2958"},"institutions":[{"id":"https://openalex.org/I4210106489","display_name":"National Heart Lung and Blood Institute","ror":"https://ror.org/012pb6c26","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210106489"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gerhard K\u00f6nig","raw_affiliation_strings":["National Institutes of Health, National Heart, Lung and Blood Institute, Laboratory of Computational Biology, 5635 Fishers Lane, T-900 Suite, Rockville, MD 20852, USA. gerhard.koenig@nih.gov","National Institutes of Health \u2013 National Heart, Lung and Blood Institute, Laboratory of Computational Biology"],"affiliations":[{"raw_affiliation_string":"National Institutes of Health, National Heart, Lung and Blood Institute, Laboratory of Computational Biology, 5635 Fishers Lane, T-900 Suite, Rockville, MD 20852, USA. gerhard.koenig@nih.gov","institution_ids":["https://openalex.org/I4210106489","https://openalex.org/I1299303238"]},{"raw_affiliation_string":"National Institutes of Health \u2013 National Heart, Lung and Blood Institute, Laboratory of Computational Biology","institution_ids":["https://openalex.org/I1299303238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079782789","display_name":"Bernard R. Brooks","orcid":"https://orcid.org/0000-0002-3586-2730"},"institutions":[{"id":"https://openalex.org/I4210106489","display_name":"National Heart Lung and Blood Institute","ror":"https://ror.org/012pb6c26","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210106489"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bernard R. Brooks","raw_affiliation_strings":["National Institutes of Health, National Heart, Lung and Blood Institute, Laboratory of Computational Biology, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA","National Institutes of Health \u2013 National Heart, Lung and Blood Institute, Laboratory of Computational Biology"],"affiliations":[{"raw_affiliation_string":"National Institutes of Health, National Heart, Lung and Blood Institute, Laboratory of Computational Biology, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA","institution_ids":["https://openalex.org/I4210106489","https://openalex.org/I1299303238"]},{"raw_affiliation_string":"National Institutes of Health \u2013 National Heart, Lung and Blood Institute, Laboratory of Computational Biology","institution_ids":["https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5027168981"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210106489"],"apc_list":{"value":2890,"currency":"EUR","value_usd":3690},"apc_paid":null,"fwci":1.549,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.81607027,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"26","issue":"5","first_page":"543","last_page":"550"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11809","display_name":"Advanced NMR Techniques and Applications","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9975000023841858,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/thermodynamic-integration","display_name":"Thermodynamic integration","score":0.7375749945640564},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.6181241869926453},{"id":"https://openalex.org/keywords/solvation","display_name":"Solvation","score":0.6155722737312317},{"id":"https://openalex.org/keywords/mean-squared-error","display_name":"Mean squared error","score":0.5557587742805481},{"id":"https://openalex.org/keywords/root-mean-square","display_name":"Root mean square","score":0.5101871490478516},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.464994341135025},{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.4621603488922119},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.4606720209121704},{"id":"https://openalex.org/keywords/deprotonation","display_name":"Deprotonation","score":0.42915740609169006},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.4239645302295685},{"id":"https://openalex.org/keywords/square-root","display_name":"Square root","score":0.4173422157764435},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.3727725148200989},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3192557096481323},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.29649731516838074},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2582523822784424},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.20649170875549316},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.19321870803833008},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.12119287252426147},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.09790411591529846},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.09330326318740845}],"concepts":[{"id":"https://openalex.org/C141780669","wikidata":"https://www.wikidata.org/wiki/Q7783161","display_name":"Thermodynamic integration","level":3,"score":0.7375749945640564},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6181241869926453},{"id":"https://openalex.org/C148093993","wikidata":"https://www.wikidata.org/wiki/Q739398","display_name":"Solvation","level":3,"score":0.6155722737312317},{"id":"https://openalex.org/C139945424","wikidata":"https://www.wikidata.org/wiki/Q1940696","display_name":"Mean squared error","level":2,"score":0.5557587742805481},{"id":"https://openalex.org/C71907059","wikidata":"https://www.wikidata.org/wiki/Q223323","display_name":"Root mean square","level":2,"score":0.5101871490478516},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.464994341135025},{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.4621603488922119},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.4606720209121704},{"id":"https://openalex.org/C118629725","wikidata":"https://www.wikidata.org/wiki/Q2686738","display_name":"Deprotonation","level":3,"score":0.42915740609169006},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.4239645302295685},{"id":"https://openalex.org/C11577676","wikidata":"https://www.wikidata.org/wiki/Q134237","display_name":"Square root","level":2,"score":0.4173422157764435},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.3727725148200989},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3192557096481323},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.29649731516838074},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2582523822784424},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.20649170875549316},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.19321870803833008},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.12119287252426147},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.09790411591529846},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.09330326318740845},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":"D011485","descriptor_name":"Protein Binding","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":"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":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","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":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1007/s10822-011-9525-y","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s10822-011-9525-y","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:22198474","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22198474","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},{"id":"pmh:oai:europepmc.org:2586191","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3584352","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3584352","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3584352","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Comput Aided Mol Des","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:3584352","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3584352","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Comput Aided Mol Des","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1966363041","https://openalex.org/W1968755416","https://openalex.org/W1970690135","https://openalex.org/W1970973025","https://openalex.org/W1972361027","https://openalex.org/W1976499671","https://openalex.org/W1991794210","https://openalex.org/W1992434579","https://openalex.org/W1997250922","https://openalex.org/W2004640547","https://openalex.org/W2018872041","https://openalex.org/W2027639883","https://openalex.org/W2028702957","https://openalex.org/W2035687084","https://openalex.org/W2048541167","https://openalex.org/W2051419785","https://openalex.org/W2057653269","https://openalex.org/W2068465600","https://openalex.org/W2070753604","https://openalex.org/W2071231667","https://openalex.org/W2071963550","https://openalex.org/W2075720910","https://openalex.org/W2088396668","https://openalex.org/W2103636724","https://openalex.org/W2120795798","https://openalex.org/W2125581050","https://openalex.org/W2128494768","https://openalex.org/W2132262459","https://openalex.org/W2140151763","https://openalex.org/W2162166182"],"related_works":["https://openalex.org/W2030642920","https://openalex.org/W4241389587","https://openalex.org/W2314667616","https://openalex.org/W2610220566","https://openalex.org/W2061769724","https://openalex.org/W2347918039","https://openalex.org/W2016437526","https://openalex.org/W2392717426","https://openalex.org/W2069750807","https://openalex.org/W2607969196"],"abstract_inverted_index":null,"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}
