{"id":"https://openalex.org/W4410567690","doi":"https://doi.org/10.1021/acs.jcim.5c00554","title":"FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks","display_name":"FE-ToolKit: A Versatile Software Suite for Analysis of High-Dimensional Free Energy Surfaces and Alchemical Free Energy Networks","publication_year":2025,"publication_date":"2025-05-21","ids":{"openalex":"https://openalex.org/W4410567690","doi":"https://doi.org/10.1021/acs.jcim.5c00554","pmid":"https://pubmed.ncbi.nlm.nih.gov/40394984","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/12232920"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00554","doi":"https://doi.org/10.1021/acs.jcim.5c00554","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00554","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00554","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00554","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007304685","display_name":"Timothy J. Giese","orcid":"https://orcid.org/0000-0002-0653-9168","observed_orcids":["https://orcid.org/0000-0002-0653-9168"]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy J. Giese","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","Rutgers University"],"raw_orcid":"https://orcid.org/0000-0002-0653-9168","affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":[]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079128702","display_name":"Ryan Snyder","orcid":"https://orcid.org/0009-0009-6703-3652","observed_orcids":["https://orcid.org/0009-0009-6703-3652"]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Snyder","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","Rutgers University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":[]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000602283","display_name":"Zeke A. Piskulich","orcid":"https://orcid.org/0000-0003-0304-305X","observed_orcids":["https://orcid.org/0000-0003-0304-305X"]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zeke Piskulich","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","Rutgers University"],"raw_orcid":"https://orcid.org/0000-0003-0304-305X","affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":[]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041716603","display_name":"German Patricio Barletta","orcid":"https://orcid.org/0000-0002-0806-0812","observed_orcids":["https://orcid.org/0000-0002-0806-0812"]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"German P. Barletta","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","Rutgers University"],"raw_orcid":"https://orcid.org/0000-0002-0806-0812","affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":[]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023371583","display_name":"Shi Zhang","orcid":"https://orcid.org/0000-0002-0281-9314","observed_orcids":["https://orcid.org/0000-0002-0281-9314"]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shi Zhang","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","Rutgers University"],"raw_orcid":"https://orcid.org/0000-0002-0281-9314","affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":[]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013132730","display_name":"Erika McCarthy","orcid":"https://orcid.org/0000-0001-8089-0207","observed_orcids":["https://orcid.org/0000-0001-8089-0207"]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Erika McCarthy","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","Rutgers University"],"raw_orcid":"https://orcid.org/0000-0001-8089-0207","affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":[]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008102135","display_name":"\u015e\u00f6len Ekesan","orcid":"https://orcid.org/0000-0002-5598-5754","observed_orcids":["https://orcid.org/0000-0002-5598-5754"]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"\u015e\u00f6len Ekesan","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","Rutgers University"],"raw_orcid":"https://orcid.org/0000-0002-5598-5754","affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":[]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076436548","display_name":"Darrin M. York","orcid":"https://orcid.org/0000-0002-9193-7055","observed_orcids":["https://orcid.org/0000-0002-9193-7055"]},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Darrin M. York","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","Rutgers University"],"raw_orcid":"https://orcid.org/0000-0002-9193-7055","affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":[]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I102322142"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5076436548"],"corresponding_institution_ids":["https://openalex.org/I102322142"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":{"value":4500,"currency":"USD","value_usd":4500},"fwci":2.9217,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.91125489,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"65","issue":"11","first_page":"5273","last_page":"5279"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.7416999936103821,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.7416999936103821,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.11129999905824661,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.08579999953508377,"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/free-energy-landscape","display_name":"free energy landscape","score":0.9829999804496765},{"id":"https://openalex.org/keywords/minimum-free-energy-path","display_name":"minimum free energy path","score":0.9240000247955322},{"id":"https://openalex.org/keywords/umbrella-sampling","display_name":"umbrella sampling","score":0.9089999794960022},{"id":"https://openalex.org/keywords/string-method","display_name":"string method","score":0.9779999852180481},{"id":"https://openalex.org/keywords/ligand-binding-free-energy","display_name":"ligand binding free energy","score":0.6600000262260437},{"id":"https://openalex.org/keywords/ligand-ranking","display_name":"ligand ranking","score":0.609000027179718},{"id":"https://openalex.org/keywords/software-suite","display_name":"software suite","score":0.38100001215934753}],"concepts":[{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.8524149656295776},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.6743001937866211},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6421725749969482},{"id":"https://openalex.org/C174468945","wikidata":"https://www.wikidata.org/wiki/Q39689","display_name":"Alchemy","level":2,"score":0.6080561876296997},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6047124266624451},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.5364407300949097},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.3337171673774719},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.22370034456253052},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.09802970290184021},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09423750638961792},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.08636474609375},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.08063915371894836},{"id":"https://openalex.org/C52119013","wikidata":"https://www.wikidata.org/wiki/Q50637","display_name":"Art history","level":1,"score":0.07886651158332825},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.5c00554","doi":"https://doi.org/10.1021/acs.jcim.5c00554","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00554","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00554","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40394984","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40394984","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 chemical information and modeling","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12232920","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12232920/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.5c00554","doi":"https://doi.org/10.1021/acs.jcim.5c00554","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00554","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00554","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1122314324","display_name":"Collaborative Research: Frameworks: Interoperable High-Performance Classical, Machine Learning and Quantum Free Energy Methods in AMBER","funder_award_id":"2209718","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1912064254","display_name":"Track 4:  Advanced CI Coordination Ecosystem: Monitoring and Measurement Services","funder_award_id":"2137603","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4006316252","display_name":"Track 1: ACCESS Resource Allocations Marketplace and Platform Services (RAMPS)","funder_award_id":"2138259","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4676224565","display_name":"ACO: An Open CI Ecosystem to Advance Scientific Discovery (OpenCI)","funder_award_id":"2138296","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G509285653","display_name":"Track 3: COre National Ecosystem for CyberinfrasTructure (CONECT)","funder_award_id":"2138307","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8300691027","display_name":"Track 2: Customized Multi-tier Assistance, Training, and Computational Help (MATCH) for End User ACCESS to CI","funder_award_id":"2138286","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G9000866635","display_name":"Computational Enzymology to Study Diverse Catalytic Strategies of RNA","funder_award_id":"R01GM062248","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G9000870718","display_name":"Next-generation alchemical free energy methods and quantum/machine-learning models for drug discovery","funder_award_id":"R01GM107485","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410567690.pdf","grobid_xml":"https://content.openalex.org/works/W4410567690.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W83927685","https://openalex.org/W1964758803","https://openalex.org/W1968994875","https://openalex.org/W1983132551","https://openalex.org/W1986614779","https://openalex.org/W1989753444","https://openalex.org/W1993177346","https://openalex.org/W1995023752","https://openalex.org/W2005313434","https://openalex.org/W2024400312","https://openalex.org/W2024762727","https://openalex.org/W2048811205","https://openalex.org/W2049738344","https://openalex.org/W2063206968","https://openalex.org/W2075956726","https://openalex.org/W2076888175","https://openalex.org/W2086474098","https://openalex.org/W2112154906","https://openalex.org/W2143171629","https://openalex.org/W2144946183","https://openalex.org/W2155554859","https://openalex.org/W2321157445","https://openalex.org/W2413165234","https://openalex.org/W2562368273","https://openalex.org/W2593105084","https://openalex.org/W2614931299","https://openalex.org/W2625712932","https://openalex.org/W2759770439","https://openalex.org/W2772641670","https://openalex.org/W2784756177","https://openalex.org/W2891791233","https://openalex.org/W2896297247","https://openalex.org/W2912364028","https://openalex.org/W2972646529","https://openalex.org/W3043456144","https://openalex.org/W3087004338","https://openalex.org/W3088895708","https://openalex.org/W3126967313","https://openalex.org/W3136228320","https://openalex.org/W3148477737","https://openalex.org/W3207860887","https://openalex.org/W4223544812","https://openalex.org/W4283029539","https://openalex.org/W4293112991","https://openalex.org/W4307431859","https://openalex.org/W4310573576","https://openalex.org/W4313830069","https://openalex.org/W4318035807","https://openalex.org/W4323320228","https://openalex.org/W4367597988","https://openalex.org/W4387334097","https://openalex.org/W4387440676","https://openalex.org/W4391895891","https://openalex.org/W4395677718","https://openalex.org/W4399499024","https://openalex.org/W4399880623","https://openalex.org/W4403064227","https://openalex.org/W4408914802","https://openalex.org/W6823690907"],"related_works":["https://openalex.org/W6911497961","https://openalex.org/W7163001191","https://openalex.org/W3201597079","https://openalex.org/W7084383803","https://openalex.org/W7130607837","https://openalex.org/W3096455667","https://openalex.org/W4387334097","https://openalex.org/W7202321607","https://openalex.org/W6894116413","https://openalex.org/W6892344879"],"abstract_inverted_index":{"Free":[0],"energy":[1,24,55,99,103,108],"simulations":[2],"play":[3],"a":[4,89],"pivotal":[5],"role":[6],"in":[7],"diverse":[8],"biological":[9],"applications,":[10],"including":[11],"enzyme":[12],"design,":[13],"drug":[14],"discovery,":[15],"and":[16,76,105],"biomolecular":[17],"engineering.":[18],"The":[19,61],"characterization":[20],"of":[21,42,64,78,97],"high-dimensional":[22],"free":[23,44,54,98,102,107],"surfaces":[25],"underlying":[26],"complex":[27],"enzymatic":[28],"mechanisms":[29],"necessitates":[30],"extensive":[31],"sampling":[32,35],"through":[33],"umbrella":[34],"or":[36],"string":[37],"method":[38],"simulations.":[39],"Accurate":[40],"ranking":[41],"target-binding":[43],"energies":[45],"across":[46],"large":[47],"ligand":[48],"libraries":[49],"relies":[50],"on":[51,68],"comprehensive":[52],"alchemical":[53,106],"calculations":[56],"organized":[57],"into":[58],"thermodynamic":[59],"networks.":[60],"predictive":[62],"accuracy":[63],"these":[65],"methods":[66],"hinges":[67],"robust,":[69],"scalable":[70],"tools":[71],"for":[72,93],"networkwide":[73],"data":[74],"analysis":[75,96],"extraction":[77],"physical":[79],"properties":[80],"from":[81],"heterogeneous":[82],"simulation":[83],"data.":[84],"Here,":[85],"we":[86],"introduce":[87],"FE-ToolKit,":[88],"versatile":[90],"software":[91],"suite":[92],"the":[94],"automated":[95],"surfaces,":[100],"minimum":[101],"paths,":[104],"networks":[109],"(thermodynamic":[110],"graphs).":[111]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":2}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2025-05-22T00:00:00"}