{"id":"https://openalex.org/W3004098428","doi":"https://doi.org/10.1007/s10822-020-00290-5","title":"The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations","display_name":"The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations","publication_year":2020,"publication_date":"2020-01-26","ids":{"openalex":"https://openalex.org/W3004098428","doi":"https://doi.org/10.1007/s10822-020-00290-5","mag":"3004098428","pmid":"https://pubmed.ncbi.nlm.nih.gov/31984465"},"language":"en","primary_location":{"id":"doi:10.1007/s10822-020-00290-5","doi":"https://doi.org/10.1007/s10822-020-00290-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-020-00290-5","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-020-00290-5.pdf","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,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","medline","norway-1","poland-70","russia-white-list-1"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10822-020-00290-5.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026440664","display_name":"Andrea Rizzi","orcid":"https://orcid.org/0000-0001-7693-2013","observed_orcids":["https://orcid.org/0000-0001-7693-2013"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andrea Rizzi","raw_affiliation_strings":["Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. andrea.rizzi@choderalab.org","Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA. andrea.rizzi@choderalab.org","Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA","Tri-Institutional Training Program in Computational Biology and Medicine, New York, USA"],"raw_orcid":"https://orcid.org/0000-0001-7693-2013","affiliations":[{"raw_affiliation_string":"Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. andrea.rizzi@choderalab.org","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA. andrea.rizzi@choderalab.org","institution_ids":[]},{"raw_affiliation_string":"Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Tri-Institutional Training Program in Computational Biology and Medicine, New York, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069412253","display_name":"Travis Jensen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Travis Jensen","raw_affiliation_strings":["Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80309, USA","Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80309, USA","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, USA","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090325434","display_name":"David R. Slochower","orcid":"https://orcid.org/0000-0003-3928-5050","observed_orcids":["https://orcid.org/0000-0003-3928-5050"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David R. Slochower","raw_affiliation_strings":["Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA","Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA"],"raw_orcid":"https://orcid.org/0000-0003-3928-5050","affiliations":[{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056535696","display_name":"Matteo Aldeghi","orcid":"https://orcid.org/0000-0003-0019-8806","observed_orcids":["https://orcid.org/0000-0003-0019-8806"]},"institutions":[{"id":"https://openalex.org/I4210131661","display_name":"Max Planck Institute for Biophysical Chemistry","ror":"https://ror.org/03e76ya46","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210131661","https://openalex.org/I4387154714"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matteo Aldeghi","raw_affiliation_strings":["Max Planck Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group, G\u00f6ttingen, Germany"],"raw_orcid":"https://orcid.org/0000-0003-0019-8806","affiliations":[{"raw_affiliation_string":"Max Planck Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I4210131661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005333819","display_name":"Vytautas Gapsys","orcid":"https://orcid.org/0000-0002-6761-7780","observed_orcids":["https://orcid.org/0000-0002-6761-7780"]},"institutions":[{"id":"https://openalex.org/I4210131661","display_name":"Max Planck Institute for Biophysical Chemistry","ror":"https://ror.org/03e76ya46","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210131661","https://openalex.org/I4387154714"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Vytautas Gapsys","raw_affiliation_strings":["Max Planck Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group, G\u00f6ttingen, Germany"],"raw_orcid":"https://orcid.org/0000-0002-6761-7780","affiliations":[{"raw_affiliation_string":"Max Planck Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I4210131661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091563245","display_name":"Dimitris Ntekoumes","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I206127235","display_name":"Academy of Athens","ror":"https://ror.org/00qsdn986","country_code":"GR","type":"education","lineage":["https://openalex.org/I206127235"]},{"id":"https://openalex.org/I4210093138","display_name":"Biomedical Research Foundation of the Academy of Athens","ror":"https://ror.org/00gban551","country_code":"GR","type":"nonprofit","lineage":["https://openalex.org/I4210093138"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Dimitris Ntekoumes","raw_affiliation_strings":["Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece","Biomedical Research Foundation, Academy of Athens, Athens, Greece"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece","institution_ids":["https://openalex.org/I206127235","https://openalex.org/I4210093138"]},{"raw_affiliation_string":"Biomedical Research Foundation, Academy of Athens, Athens, Greece","institution_ids":["https://openalex.org/I206127235","https://openalex.org/I4210093138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074528876","display_name":"Stefano Bosisio","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stefano Bosisio","raw_affiliation_strings":["EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK","EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058688565","display_name":"Michail Papadourakis","orcid":"https://orcid.org/0000-0002-9969-5871","observed_orcids":["https://orcid.org/0000-0002-9969-5871"]},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Michail Papadourakis","raw_affiliation_strings":["EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK","EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011259040","display_name":"Niel M. Henriksen","orcid":"https://orcid.org/0000-0002-7916-0757","observed_orcids":["https://orcid.org/0000-0002-7916-0757"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4405270056","display_name":"Numerion Labs (United States)","ror":"https://ror.org/00140ty38","country_code":"US","type":"company","lineage":["https://openalex.org/I4405270056"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Niel M. Henriksen","raw_affiliation_strings":["Atomwise, 717 Market St Suite 800, San Francisco, CA, 94103, USA","Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA","Atomwise, San Francisco, USA","Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA"],"raw_orcid":"https://orcid.org/0000-0002-7916-0757","affiliations":[{"raw_affiliation_string":"Atomwise, 717 Market St Suite 800, San Francisco, CA, 94103, USA","institution_ids":["https://openalex.org/I4405270056"]},{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Atomwise, San Francisco, USA","institution_ids":["https://openalex.org/I4405270056"]},{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044839728","display_name":"Bert L. de Groot","orcid":"https://orcid.org/0000-0003-3570-3534","observed_orcids":["https://orcid.org/0000-0003-3570-3534"]},"institutions":[{"id":"https://openalex.org/I4210131661","display_name":"Max Planck Institute for Biophysical Chemistry","ror":"https://ror.org/03e76ya46","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210131661","https://openalex.org/I4387154714"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bert L. de Groot","raw_affiliation_strings":["Max Planck Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group, G\u00f6ttingen, Germany"],"raw_orcid":"https://orcid.org/0000-0003-3570-3534","affiliations":[{"raw_affiliation_string":"Max Planck Institute for Biophysical Chemistry, Computational Biomolecular Dynamics Group, G\u00f6ttingen, Germany","institution_ids":["https://openalex.org/I4210131661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062304446","display_name":"Zoe Cournia","orcid":"https://orcid.org/0000-0001-9287-364X","observed_orcids":["https://orcid.org/0000-0001-9287-364X"]},"institutions":[{"id":"https://openalex.org/I206127235","display_name":"Academy of Athens","ror":"https://ror.org/00qsdn986","country_code":"GR","type":"education","lineage":["https://openalex.org/I206127235"]},{"id":"https://openalex.org/I4210093138","display_name":"Biomedical Research Foundation of the Academy of Athens","ror":"https://ror.org/00gban551","country_code":"GR","type":"nonprofit","lineage":["https://openalex.org/I4210093138"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Zoe Cournia","raw_affiliation_strings":["Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece","Biomedical Research Foundation, Academy of Athens, Athens, Greece"],"raw_orcid":"https://orcid.org/0000-0001-9287-364X","affiliations":[{"raw_affiliation_string":"Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527, Athens, Greece","institution_ids":["https://openalex.org/I206127235","https://openalex.org/I4210093138"]},{"raw_affiliation_string":"Biomedical Research Foundation, Academy of Athens, Athens, Greece","institution_ids":["https://openalex.org/I206127235","https://openalex.org/I4210093138"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054841813","display_name":"Alex Dickson","orcid":"https://orcid.org/0000-0002-9640-1380","observed_orcids":["https://orcid.org/0000-0002-9640-1380"]},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alex Dickson","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA","Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA","Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA","Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA"],"raw_orcid":"https://orcid.org/0000-0002-9640-1380","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, USA","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, USA","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041098529","display_name":"Julien Michel","orcid":"https://orcid.org/0000-0003-0360-1760","observed_orcids":["https://orcid.org/0000-0003-0360-1760"]},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Julien Michel","raw_affiliation_strings":["EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK","EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK"],"raw_orcid":"https://orcid.org/0000-0003-0360-1760","affiliations":[{"raw_affiliation_string":"EaStCHEM School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049982297","display_name":"Michael K. Gilson","orcid":"https://orcid.org/0000-0002-3375-1738","observed_orcids":["https://orcid.org/0000-0002-3375-1738"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael K. Gilson","raw_affiliation_strings":["Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA","Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA"],"raw_orcid":"https://orcid.org/0000-0002-3375-1738","affiliations":[{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080360440","display_name":"Michael R. Shirts","orcid":"https://orcid.org/0000-0003-3249-1097","observed_orcids":["https://orcid.org/0000-0003-3249-1097"]},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael R. Shirts","raw_affiliation_strings":["Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80309, USA","Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, USA"],"raw_orcid":"https://orcid.org/0000-0003-3249-1097","affiliations":[{"raw_affiliation_string":"Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, 80309, USA","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, USA","institution_ids":["https://openalex.org/I188538660"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007496868","display_name":"David L. Mobley","orcid":"https://orcid.org/0000-0002-1083-5533","observed_orcids":["https://orcid.org/0000-0002-1083-5533"]},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David L. Mobley","raw_affiliation_strings":["Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, California, 92697, USA. dmobley@uci.edu","Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, USA"],"raw_orcid":"https://orcid.org/0000-0002-1083-5533","affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, California, 92697, USA. dmobley@uci.edu","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083925073","display_name":"John D. Chodera","orcid":"https://orcid.org/0000-0003-0542-119X","observed_orcids":["https://orcid.org/0000-0003-0542-119X"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John D. Chodera","raw_affiliation_strings":["Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. john.chodera@choderalab.org","Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA"],"raw_orcid":"https://orcid.org/0000-0003-0542-119X","affiliations":[{"raw_affiliation_string":"Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. john.chodera@choderalab.org","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, USA","institution_ids":["https://openalex.org/I1334819555"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5007496868","https://openalex.org/A5026440664","https://openalex.org/A5083925073"],"corresponding_institution_ids":["https://openalex.org/I1334819555","https://openalex.org/I204250578"],"apc_list":{"value":3260,"currency":"USD","value_usd":3260},"apc_paid":{"value":3260,"currency":"USD","value_usd":3260},"fwci":11.3172,"has_fulltext":true,"cited_by_count":122,"citation_normalized_percentile":{"value":0.98773484,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"34","issue":"5","first_page":"601","last_page":"633"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.951200008392334,"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":0.951200008392334,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.019099999219179153,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.012400000356137753,"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/binding-free-energy","display_name":"binding free energy","score":0.7440000176429749},{"id":"https://openalex.org/keywords/alchemical-free-energy-methods","display_name":"alchemical free energy methods","score":0.609000027179718},{"id":"https://openalex.org/keywords/potential-of-mean-force","display_name":"potential of mean force","score":0.9160000085830688},{"id":"https://openalex.org/keywords/weighted-ensemble","display_name":"weighted ensemble","score":0.7390000224113464},{"id":"https://openalex.org/keywords/cucurbit-8-uril","display_name":"cucurbit[8]uril","score":0.9110000133514404},{"id":"https://openalex.org/keywords/quinine","display_name":"quinine","score":0.6869999766349792},{"id":"https://openalex.org/keywords/parallel-tempering","display_name":"parallel tempering","score":0.7310000061988831},{"id":"https://openalex.org/keywords/bias-and-variance","display_name":"bias and variance","score":0.5460000038146973},{"id":"https://openalex.org/keywords/method-comparison","display_name":"method comparison","score":0.3440000116825104},{"id":"https://openalex.org/keywords/reproducibility","display_name":"reproducibility","score":0.7739999890327454},{"id":"https://openalex.org/keywords/force-field-parameters","display_name":"force field parameters","score":0.5630000233650208},{"id":"https://openalex.org/keywords/atomic-charges","display_name":"atomic charges","score":0.8949999809265137}],"concepts":[{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.7001607418060303},{"id":"https://openalex.org/C200601418","wikidata":"https://www.wikidata.org/wiki/Q2193887","display_name":"Reliability engineering","level":1,"score":0.6430462598800659},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.5387450456619263},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.41144245862960815},{"id":"https://openalex.org/C39432304","wikidata":"https://www.wikidata.org/wiki/Q188847","display_name":"Environmental science","level":0,"score":0.407623291015625},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38418176770210266},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.36940592527389526},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24205705523490906},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.21750319004058838},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11826443672180176},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.10335800051689148},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0751810073852539},{"id":"https://openalex.org/C94915269","wikidata":"https://www.wikidata.org/wiki/Q1834857","display_name":"Detector","level":2,"score":0.0},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001952","descriptor_name":"Bridged-Ring Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001952","descriptor_name":"Bridged-Ring Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001952","descriptor_name":"Bridged-Ring Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007093","descriptor_name":"Imidazoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007093","descriptor_name":"Imidazoles","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007093","descriptor_name":"Imidazoles","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":"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":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","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":"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":"D047028","descriptor_name":"Macrocyclic Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D047028","descriptor_name":"Macrocyclic Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D047028","descriptor_name":"Macrocyclic Compounds","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055585","descriptor_name":"Physical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055585","descriptor_name":"Physical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055585","descriptor_name":"Physical Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1007/s10822-020-00290-5","doi":"https://doi.org/10.1007/s10822-020-00290-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-020-00290-5","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-020-00290-5.pdf","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,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","medline","norway-1","poland-70","russia-white-list-1"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},{"id":"doi:10.1101/795005","doi":"https://doi.org/10.1101/795005","is_oa":true,"landing_page_url":"https://doi.org/10.1101/795005","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2020/01/03/795005.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:31984465","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31984465","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,"listed_in":[],"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":"Journal Article"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/f319a492-df00-4b8a-a180-64ebc209c760","doi":null,"is_oa":true,"landing_page_url":"https://hdl.handle.net/20.500.11820/f319a492-df00-4b8a-a180-64ebc209c760","pdf_url":"https://www.research.ed.ac.uk/files/135033779/20200214_Michel_SAMPL6_SAMPLing_challenge_manuscript.pdf","source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"Rizzi, A, Jensen, T, Slochower, D R, Aldeghi, M, Gapsys, V, Ntekoumes, D, Bosisio, S, Papadourakis, M, Henriksen, N M, de Groot, B L, Cournia, Z, Dickson, A, Michel, J, Gilson, M K, Shirts, M R, Mobley, D L & Chodera, J D 2020, 'The SAMPL6 SAMPLing challenge : assessing the reliability and efficiency of binding free energy calculations', Journal of computer-Aided molecular design. https://doi.org/10.1007/s10822-020-00290-5","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7282318","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7282318","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt3x6032nq","doi":null,"is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/3x6032nq","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Computer-Aided Molecular Design, vol 34, iss 5","raw_type":"article"},{"id":"pmh:oai:pure.mpg.de:item_3191106","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/21.11116/0000-0005-991C-0","pdf_url":null,"source":{"id":"https://openalex.org/S4306400654","display_name":"MPG.PuRe (Max Planck Society)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"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":"Journal of Computer-Aided Molecular Design","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1007/s10822-020-00290-5","doi":"https://doi.org/10.1007/s10822-020-00290-5","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10822-020-00290-5","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10822-020-00290-5.pdf","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,"listed_in":["cwts-core","dongbi-c","doyens","jufo-1","medline","norway-1","poland-70","russia-white-list-1"],"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computer-Aided Molecular Design","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"score":0.8899999856948853,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G108378697","display_name":null,"funder_award_id":"NSRF 2014\u20132020","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1318489236","display_name":"CAREER: Computing accurate free energies for solubility, solvation, and transfer","funder_award_id":"1352608","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1337233005","display_name":null,"funder_award_id":"NSRF 2014-2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G1577988765","display_name":null,"funder_award_id":"823830","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1888088267","display_name":null,"funder_award_id":"2014-2020\u2019","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1953887145","display_name":null,"funder_award_id":"2014\u20102020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2453889086","display_name":null,"funder_award_id":"MIS 5002691","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G2628364946","display_name":null,"funder_award_id":"H2020","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G2952370546","display_name":null,"funder_award_id":"1352608","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G298708225","display_name":"Advancing predictive physical modeling through focused development of model systems to drive new modeling innovations","funder_award_id":"1r01gm124270-01a1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3471917844","display_name":"BioExcel Centre of Excellence for ComputationalBiomolecular Research","funder_award_id":"823830","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3645681628","display_name":null,"funder_award_id":"CHE 1352608","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G3940821885","display_name":"Computational alchemy for molecular design and optimization","funder_award_id":"R01GM108889","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3982398266","display_name":null,"funder_award_id":"R01GM061300","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4123512917","display_name":null,"funder_award_id":"H2020","funder_id":"https://openalex.org/F4320308269","funder_display_name":"Alexander von Humboldt-Stiftung"},{"id":"https://openalex.org/G4330362853","display_name":null,"funder_award_id":"H2020-INFRAEDI-02-2018823830","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4420342495","display_name":null,"funder_award_id":"2014-2020","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4423801172","display_name":null,"funder_award_id":"1R01GM124270-01A1","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4583515593","display_name":null,"funder_award_id":"CA008748","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4937468798","display_name":null,"funder_award_id":"H2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G539881341","display_name":null,"funder_award_id":"CHE-1352608","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"},{"id":"https://openalex.org/G5509327845","display_name":"Kinetics-Driven Drug Discovery Using Persistent Homology, Rare-Event Molecular Dynamics and Experimental Data","funder_award_id":"1761320","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G738642497","display_name":null,"funder_award_id":"GM061300","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7556015768","display_name":null,"funder_award_id":"P30 CA008748","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7796364618","display_name":null,"funder_award_id":"P30 CA008748","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G78272153","display_name":null,"funder_award_id":"R01 GM130794","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8272707588","display_name":null,"funder_award_id":"DMS 1761320","funder_id":"https://openalex.org/F4320335353","funder_display_name":"National Science Foundation of Sri Lanka"},{"id":"https://openalex.org/G828594454","display_name":null,"funder_award_id":"T32 GM 065103","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G834416952","display_name":null,"funder_award_id":"R01GM124270","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8567706437","display_name":null,"funder_award_id":"H2020-INFRAEDI-02-2018- 823830","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G8592912233","display_name":null,"funder_award_id":"823830","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8858395165","display_name":null,"funder_award_id":"H2020","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8903667313","display_name":null,"funder_award_id":"823830","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G9000003249","display_name":null,"funder_award_id":"CA008748","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000053173","display_name":null,"funder_award_id":"GM061300","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000342653","display_name":null,"funder_award_id":"R01GM130794","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000856728","display_name":"Cancer Center Support Grant","funder_award_id":"P30CA008748","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320308269","display_name":"Alexander von Humboldt-Stiftung","ror":"https://ror.org/012kf4317"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320335353","display_name":"National Science Foundation of Sri Lanka","ror":"https://ror.org/010xaa060"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3004098428.pdf","grobid_xml":"https://content.openalex.org/works/W3004098428.grobid-xml"},"referenced_works_count":143,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W1034882992","https://openalex.org/W1178456644","https://openalex.org/W1553864921","https://openalex.org/W1965762256","https://openalex.org/W1970690135","https://openalex.org/W1971124985","https://openalex.org/W1971493096","https://openalex.org/W1976499671","https://openalex.org/W1976896799","https://openalex.org/W1977151908","https://openalex.org/W1977234725","https://openalex.org/W1978189250","https://openalex.org/W1978393297","https://openalex.org/W1980146313","https://openalex.org/W1981225934","https://openalex.org/W1989195611","https://openalex.org/W1990724722","https://openalex.org/W1997125900","https://openalex.org/W1997308124","https://openalex.org/W2002664623","https://openalex.org/W2003582562","https://openalex.org/W2006228399","https://openalex.org/W2013145865","https://openalex.org/W2015688756","https://openalex.org/W2017829285","https://openalex.org/W2018736104","https://openalex.org/W2021820673","https://openalex.org/W2024762727","https://openalex.org/W2025625972","https://openalex.org/W2027154929","https://openalex.org/W2027423337","https://openalex.org/W2034099569","https://openalex.org/W2035078255","https://openalex.org/W2035266068","https://openalex.org/W2035687084","https://openalex.org/W2037535298","https://openalex.org/W2038758364","https://openalex.org/W2040398799","https://openalex.org/W2041726179","https://openalex.org/W2046932130","https://openalex.org/W2047676282","https://openalex.org/W2050617474","https://openalex.org/W2051060071","https://openalex.org/W2057806291","https://openalex.org/W2061583504","https://openalex.org/W2067076385","https://openalex.org/W2067780958","https://openalex.org/W2072604508","https://openalex.org/W2072683434","https://openalex.org/W2074140794","https://openalex.org/W2087271871","https://openalex.org/W2089435371","https://openalex.org/W2091068412","https://openalex.org/W2093327248","https://openalex.org/W2103034037","https://openalex.org/W2114227821","https://openalex.org/W2122759946","https://openalex.org/W2126728600","https://openalex.org/W2129213941","https://openalex.org/W2138434873","https://openalex.org/W2139447954","https://openalex.org/W2140151763","https://openalex.org/W2146462263","https://openalex.org/W2147988069","https://openalex.org/W2147993766","https://openalex.org/W2149655632","https://openalex.org/W2149801992","https://openalex.org/W2150981663","https://openalex.org/W2151022427","https://openalex.org/W2154670681","https://openalex.org/W2155554859","https://openalex.org/W2155858732","https://openalex.org/W2157135163","https://openalex.org/W2311078281","https://openalex.org/W2314972145","https://openalex.org/W2316723628","https://openalex.org/W2321640944","https://openalex.org/W2331161041","https://openalex.org/W2412116265","https://openalex.org/W2492174401","https://openalex.org/W2492804765","https://openalex.org/W2515097834","https://openalex.org/W2527541313","https://openalex.org/W2528035299","https://openalex.org/W2528409486","https://openalex.org/W2540491215","https://openalex.org/W2560233715","https://openalex.org/W2564264868","https://openalex.org/W2597025763","https://openalex.org/W2599323046","https://openalex.org/W2605497580","https://openalex.org/W2734617364","https://openalex.org/W2755656231","https://openalex.org/W2757663759","https://openalex.org/W2772606519","https://openalex.org/W2774738748","https://openalex.org/W2777443976","https://openalex.org/W2795365990","https://openalex.org/W2799449009","https://openalex.org/W2800811565","https://openalex.org/W2800994818","https://openalex.org/W2804572315","https://openalex.org/W2888553603","https://openalex.org/W2889154729","https://openalex.org/W2889338353","https://openalex.org/W2890108293","https://openalex.org/W2890476778","https://openalex.org/W2892182810","https://openalex.org/W2895157296","https://openalex.org/W2895630903","https://openalex.org/W2896002068","https://openalex.org/W2898134157","https://openalex.org/W2899162402","https://openalex.org/W2899481329","https://openalex.org/W2900977207","https://openalex.org/W2901357371","https://openalex.org/W2910318997","https://openalex.org/W2915248527","https://openalex.org/W2940886864","https://openalex.org/W2949223833","https://openalex.org/W2950438613","https://openalex.org/W2950669909","https://openalex.org/W2951039542","https://openalex.org/W2952635193","https://openalex.org/W2955533504","https://openalex.org/W2969038621","https://openalex.org/W2990537389","https://openalex.org/W3097977069","https://openalex.org/W3098098342","https://openalex.org/W3100565380","https://openalex.org/W3101006260","https://openalex.org/W3101060993","https://openalex.org/W3102529165","https://openalex.org/W3103967662","https://openalex.org/W3105581675","https://openalex.org/W4235088860","https://openalex.org/W4238186339","https://openalex.org/W4299550019","https://openalex.org/W6808810039","https://openalex.org/W6893893789","https://openalex.org/W6912633819","https://openalex.org/W6968844277"],"related_works":["https://openalex.org/W2033512842","https://openalex.org/W4233600955","https://openalex.org/W4322734194","https://openalex.org/W3116237489","https://openalex.org/W4404996554","https://openalex.org/W2913665393","https://openalex.org/W2369695847","https://openalex.org/W3005535424","https://openalex.org/W2994319598","https://openalex.org/W2047067935"],"abstract_inverted_index":{"Approaches":[0],"for":[1,33,69,105,132,247,366,371],"computing":[2],"small":[3,31,181,339],"molecule":[4],"binding":[5,91,117],"free":[6,92,118,175,185,368],"energies":[7],"based":[8,168],"on":[9,82,169,349],"molecular":[10],"simulations":[11,300],"are":[12,250,359],"now":[13],"regularly":[14],"being":[15],"employed":[16],"by":[17,343],"academic":[18],"and":[19,26,41,53,67,88,101,109,129,136,143,171,191,201,219,244,272,281,302,374],"industry":[20],"practitioners":[21],"to":[22,47,277,293,315],"study":[23],"receptor-ligand":[24],"systems":[25,372],"prioritize":[27],"the":[28,37,50,65,70,74,78,83,125,151,161,174,179,184,207,213,225,231,236,241,259,264,318,325,329,350,354,376],"synthesis":[29],"of":[30,39,56,85,90,124,127,140,146,173,193,206,209,321,353],"molecules":[32],"ligand":[34],"design.":[35],"Given":[36],"variety":[38],"methods":[40,58,232],"implementations":[42],"available,":[43],"it":[44],"is":[45,275],"natural":[46],"ask":[48],"how":[49],"convergence":[51,86],"rates":[52],"final":[54],"predictions":[55,120,288],"these":[57,322],"compare.":[59],"In":[60],"this":[61,253],"study,":[62],"we":[63,163,282,331],"describe":[64],"concept":[66],"results":[68,265],"SAMPL6":[71],"SAMPLing":[72],"challenge,":[73],"first":[75],"challenge":[76],"from":[77,291,328],"SAMPL":[79],"series":[80],"focusing":[81],"assessment":[84],"properties":[87],"reproducibility":[89],"energy":[93,119,130,176,186,369],"methodologies.":[94],"We":[95],"provided":[96],"parameter":[97],"files,":[98],"partial":[99,273],"charges,":[100],"multiple":[102],"initial":[103,351],"geometries":[104],"two":[106,180],"octa-acid":[107],"(OA)":[108],"one":[110],"cucurbit[8]uril":[111],"(CB8)":[112],"host-guest":[113],"systems.":[114],"Participants":[115],"submitted":[116],"as":[121,203],"a":[122,204,344],"function":[123,205],"number":[126,208],"force":[128,142,195,269],"evaluations":[131],"seven":[133],"different":[134],"alchemical":[135,190],"physical-pathway":[137],"(i.e.,":[138],"potential":[139,192],"mean":[141,194],"weighted":[144],"ensemble":[145,384],"trajectories)":[147],"methodologies":[148],"implemented":[149],"with":[150,189,212,297],"GROMACS,":[152],"AMBER,":[153],"NAMD,":[154],"or":[155],"OpenMM":[156],"simulation":[157],"engines.":[158],"To":[159],"rank":[160],"methods,":[162],"developed":[164],"an":[165],"efficiency":[166],"statistic":[167],"bias":[170,202,346],"variance":[172,200],"estimates.":[177],"For":[178,252],"OA":[182],"binders,":[183],"estimates":[187],"computed":[188],"approaches":[196],"show":[197],"relatively":[198],"similar":[199],"energy/force":[210],"evaluations,":[211],"attach-pull-release":[214],"(APR),":[215],"GROMACS":[216],"expanded":[217,383],"ensemble,":[218],"NAMD":[220],"double":[221],"decoupling":[222],"submissions":[223],"obtaining":[224],"greatest":[226],"efficiency.":[227,262],"The":[228],"differences":[229,284],"between":[230,285],"increase":[233],"when":[234],"analyzing":[235],"CB8-quinine":[237],"system,":[238,254],"where":[239],"both":[240],"guest":[242],"size":[243],"correlation":[245],"times":[246],"system":[248,303],"dynamics":[249],"greater.":[251],"nonequilibrium":[255,367],"switching":[256],"(GROMACS/NS-DS/SB)":[257],"obtained":[258],"overall":[260],"highest":[261],"Surprisingly,":[263],"suggest":[266],"that":[267,333,347,356,375],"specifying":[268],"field":[270],"parameters":[271,301],"charges":[274],"insufficient":[276],"generally":[278],"ensure":[279],"reproducibility,":[280],"observe":[283],"seemingly":[286],"converged":[287],"ranging":[289],"approximately":[290],"0.3":[292],"1.0":[294],"kcal/mol,":[295],"even":[296],"almost":[298],"identical":[299],"setup":[304],"(e.g.,":[305],"Lennard-Jones":[306],"cutoff,":[307],"ionic":[308],"composition).":[309],"Further":[310],"work":[311],"will":[312],"be":[313,341],"required":[314],"completely":[316],"identify":[317],"exact":[319],"source":[320],"discrepancies.":[323],"Among":[324],"conclusions":[326],"emerging":[327],"data,":[330],"found":[332],"Hamiltonian":[334],"replica":[335],"exchange-while":[336],"displaying":[337],"very":[338],"variance-can":[340],"affected":[342],"slowly-decaying":[345],"depends":[348],"population":[352],"replicas,":[355],"bidirectional":[357],"estimators":[358,365],"significantly":[360],"more":[361],"efficient":[362],"than":[363],"unidirectional":[364],"calculations":[370],"considered,":[373],"Berendsen":[377],"barostat":[378],"introduces":[379],"non-negligible":[380],"artifacts":[381],"in":[382],"simulations.":[385]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":24},{"year":2021,"cited_by_count":35},{"year":2020,"cited_by_count":23},{"year":2019,"cited_by_count":2}],"updated_date":"2026-10-15T10:00:46.086208","created_date":"2025-10-10T00:00:00"}