{"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"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00554","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00554","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"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"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.5c00554","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007304685","display_name":"Timothy J. Giese","orcid":"https://orcid.org/0000-0002-0653-9168"},"institutions":[{"id":"https://openalex.org/I4210096112","display_name":"Rutgers Sexual and Reproductive Health and Rights","ror":"https://ror.org/00rcvgx40","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210096112"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["NL","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"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079128702","display_name":"Ryan Snyder","orcid":"https://orcid.org/0009-0009-6703-3652"},"institutions":[{"id":"https://openalex.org/I4210096112","display_name":"Rutgers Sexual and Reproductive Health and Rights","ror":"https://ror.org/00rcvgx40","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210096112"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["NL","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"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000602283","display_name":"Zeke A. Piskulich","orcid":"https://orcid.org/0000-0003-0304-305X"},"institutions":[{"id":"https://openalex.org/I4210096112","display_name":"Rutgers Sexual and Reproductive Health and Rights","ror":"https://ror.org/00rcvgx40","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210096112"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["NL","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"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041716603","display_name":"German P. Barletta","orcid":"https://orcid.org/0000-0002-0806-0812"},"institutions":[{"id":"https://openalex.org/I4210096112","display_name":"Rutgers Sexual and Reproductive Health and Rights","ror":"https://ror.org/00rcvgx40","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210096112"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["NL","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"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023371583","display_name":"Shi Zhang","orcid":"https://orcid.org/0000-0002-0281-9314"},"institutions":[{"id":"https://openalex.org/I4210096112","display_name":"Rutgers Sexual and Reproductive Health and Rights","ror":"https://ror.org/00rcvgx40","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210096112"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["NL","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"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013132730","display_name":"Erika McCarthy","orcid":"https://orcid.org/0000-0001-8089-0207"},"institutions":[{"id":"https://openalex.org/I4210096112","display_name":"Rutgers Sexual and Reproductive Health and Rights","ror":"https://ror.org/00rcvgx40","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210096112"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["NL","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"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008102135","display_name":"\u015e\u00f6len Ekesan","orcid":"https://orcid.org/0000-0002-5598-5754"},"institutions":[{"id":"https://openalex.org/I4210096112","display_name":"Rutgers Sexual and Reproductive Health and Rights","ror":"https://ror.org/00rcvgx40","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210096112"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["NL","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"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076436548","display_name":"Darrin M. York","orcid":"https://orcid.org/0000-0002-9193-7055"},"institutions":[{"id":"https://openalex.org/I4210096112","display_name":"Rutgers Sexual and Reproductive Health and Rights","ror":"https://ror.org/00rcvgx40","country_code":"NL","type":"other","lineage":["https://openalex.org/I4210096112"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["NL","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"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5076436548"],"corresponding_institution_ids":["https://openalex.org/I4210096112","https://openalex.org/I4210098931"],"apc_list":null,"apc_paid":null,"fwci":2.0746,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.86698827,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.995199978351593,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.8524149656295776},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.6743001937866211},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6421725749969482},{"id":"https://openalex.org/keywords/alchemy","display_name":"Alchemy","score":0.6080561876296997},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6047124266624451},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.5364407300949097},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.3337171673774719},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.22370034456253052},{"id":"https://openalex.org/keywords/art","display_name":"Art","score":0.09802970290184021},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09423750638961792},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.08636474609375},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.08063915371894836},{"id":"https://openalex.org/keywords/art-history","display_name":"Art history","score":0.07886651158332825}],"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","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},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","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","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00554","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"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","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,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12232920","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12232920","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.5c00554","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00554","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"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":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.75}],"awards":[{"id":"https://openalex.org/G1122314324","display_name":null,"funder_award_id":"2209718","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6436539719","display_name":null,"funder_award_id":"GM107485","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8852971926","display_name":null,"funder_award_id":"GM62248","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":60,"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/W3105581675","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/W1516095885","https://openalex.org/W2158573927","https://openalex.org/W4231704780","https://openalex.org/W2108921801","https://openalex.org/W4206079007","https://openalex.org/W2398058485","https://openalex.org/W254965819","https://openalex.org/W4205365843","https://openalex.org/W3156231268","https://openalex.org/W3101967630"],"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":2},{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
