{"id":"https://openalex.org/W7128843748","doi":"https://doi.org/10.1021/acs.jcim.5c02932","title":"Doing More with Less: Accurate and Scalable Ligand Free Energy Calculations by Focusing on the Binding Site","display_name":"Doing More with Less: Accurate and Scalable Ligand Free Energy Calculations by Focusing on the Binding Site","publication_year":2026,"publication_date":"2026-02-13","ids":{"openalex":"https://openalex.org/W7128843748","doi":"https://doi.org/10.1021/acs.jcim.5c02932","pmid":"https://pubmed.ncbi.nlm.nih.gov/41685578"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02932","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02932","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02932?ref=article_openPDF","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://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02932?ref=article_openPDF","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090495544","display_name":"David Alencar Araripe","orcid":"https://orcid.org/0000-0002-5104-1959"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]},{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["NL","SE"],"is_corresponding":false,"raw_author_name":"David Alencar Araripe","raw_affiliation_strings":["Department of Cell & Molecular Biology","Department of Medicinal Chemistry, Photopharmacology and Imaging, Groningen Research Institute of Pharmacy (GRIP), Faculty of Science and Engineering, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands","Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands","Uppsala University, Biomedical Center"],"raw_orcid":"https://orcid.org/0000-0002-5104-1959","affiliations":[{"raw_affiliation_string":"Department of Cell & Molecular Biology","institution_ids":[]},{"raw_affiliation_string":"Department of Medicinal Chemistry, Photopharmacology and Imaging, Groningen Research Institute of Pharmacy (GRIP), Faculty of Science and Engineering, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171","https://openalex.org/I121797337"]},{"raw_affiliation_string":"Uppsala University, Biomedical Center","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5125994674","display_name":"Alejandro D\u00edaz-Holgu\u00edn","orcid":null},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Alejandro D\u00edaz-Holgu\u00edn","raw_affiliation_strings":["Department of Cell & Molecular Biology","Uppsala University, Biomedical Center"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell & Molecular Biology","institution_ids":[]},{"raw_affiliation_string":"Uppsala University, Biomedical Center","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074083544","display_name":"Antti Poso","orcid":"https://orcid.org/0000-0003-4196-4204"},"institutions":[{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Antti Poso","raw_affiliation_strings":["School of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland"],"raw_orcid":"https://orcid.org/0000-0003-4196-4204","affiliations":[{"raw_affiliation_string":"School of Pharmacy, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland","institution_ids":["https://openalex.org/I175532246"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088996741","display_name":"Gerard J. P. van Westen","orcid":"https://orcid.org/0000-0003-0717-1817"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Gerard J. P. van Westen","raw_affiliation_strings":["Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0003-0717-1817","affiliations":[{"raw_affiliation_string":"Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171","https://openalex.org/I121797337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111764714","display_name":"Johan \u00c5qvist","orcid":null},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Johan \u00c5qvist","raw_affiliation_strings":["Department of Cell & Molecular Biology","Uppsala University, Biomedical Center"],"raw_orcid":"https://orcid.org/0000-0003-2091-0610","affiliations":[{"raw_affiliation_string":"Department of Cell & Molecular Biology","institution_ids":[]},{"raw_affiliation_string":"Uppsala University, Biomedical Center","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5125900483","display_name":"Hugo Guti\u00e9rrez-de-Ter\u00e1n","orcid":null},"institutions":[{"id":"https://openalex.org/I123387679","display_name":"Uppsala University","ror":"https://ror.org/048a87296","country_code":"SE","type":"education","lineage":["https://openalex.org/I123387679"]},{"id":"https://openalex.org/I4210094696","display_name":"Stichting MS Research","ror":"https://ror.org/00qeet526","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I4210094696"]},{"id":"https://openalex.org/I4210140437","display_name":"Nanomaterials and Nanotechnology Research Center","ror":"https://ror.org/03ppnws78","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210140437"]},{"id":"https://openalex.org/I4210166274","display_name":"Instituto de Investigaci\u00f3n Sanitaria del Principado de Asturias","ror":"https://ror.org/05xzb7x97","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210166274"]}],"countries":["ES","NL","SE"],"is_corresponding":true,"raw_author_name":"Hugo Guti\u00e9rrez-de-Ter\u00e1n","raw_affiliation_strings":["Department of Cell & Molecular Biology","MODSIM Pharma AI B.V., Industrieweg 9, 2254AE Voorschoten, The Netherlands","Nanomaterials and Nanotechnology Research Center (CINN), CSIC-University of Oviedo-Principado de Asturias, and Health Research Institute of Asturias (ISPA), Av. del Hospital Universitario, s/n, ES-33011 Oviedo, Asturias, Spain","Uppsala University, Biomedical Center"],"raw_orcid":"https://orcid.org/0000-0003-0459-3491","affiliations":[{"raw_affiliation_string":"Department of Cell & Molecular Biology","institution_ids":[]},{"raw_affiliation_string":"MODSIM Pharma AI B.V., Industrieweg 9, 2254AE Voorschoten, The Netherlands","institution_ids":["https://openalex.org/I4210094696"]},{"raw_affiliation_string":"Nanomaterials and Nanotechnology Research Center (CINN), CSIC-University of Oviedo-Principado de Asturias, and Health Research Institute of Asturias (ISPA), Av. del Hospital Universitario, s/n, ES-33011 Oviedo, Asturias, Spain","institution_ids":["https://openalex.org/I4210140437","https://openalex.org/I4210166274"]},{"raw_affiliation_string":"Uppsala University, Biomedical Center","institution_ids":["https://openalex.org/I123387679"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063810062","display_name":"Willem Jespers","orcid":"https://orcid.org/0000-0002-4951-9220"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]},{"id":"https://openalex.org/I4210094696","display_name":"Stichting MS Research","ror":"https://ror.org/00qeet526","country_code":"NL","type":"nonprofit","lineage":["https://openalex.org/I4210094696"]},{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Willem Jespers","raw_affiliation_strings":["Department of Medicinal Chemistry, Photopharmacology and Imaging, Groningen Research Institute of Pharmacy (GRIP), Faculty of Science and Engineering, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands","Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands","MODSIM Pharma AI B.V., Industrieweg 9, 2254AE Voorschoten, The Netherlands"],"raw_orcid":"https://orcid.org/0000-0002-4951-9220","affiliations":[{"raw_affiliation_string":"Department of Medicinal Chemistry, Photopharmacology and Imaging, Groningen Research Institute of Pharmacy (GRIP), Faculty of Science and Engineering, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171","https://openalex.org/I121797337"]},{"raw_affiliation_string":"MODSIM Pharma AI B.V., Industrieweg 9, 2254AE Voorschoten, The Netherlands","institution_ids":["https://openalex.org/I4210094696"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5063810062","https://openalex.org/A5125900483"],"corresponding_institution_ids":["https://openalex.org/I121797337","https://openalex.org/I123387679","https://openalex.org/I169381384","https://openalex.org/I4210094696","https://openalex.org/I4210133171","https://openalex.org/I4210140437","https://openalex.org/I4210166274"],"apc_list":null,"apc_paid":null,"fwci":14.2864,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.9760181,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"66","issue":"6","first_page":"3164","last_page":"3172"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.534600019454956,"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":0.534600019454956,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.26499998569488525,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.04580000042915344,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6219000220298767},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.5964999794960022},{"id":"https://openalex.org/keywords/free-energy-perturbation","display_name":"Free energy perturbation","score":0.5898000001907349},{"id":"https://openalex.org/keywords/computational-complexity-theory","display_name":"Computational complexity theory","score":0.4830999970436096},{"id":"https://openalex.org/keywords/perturbation","display_name":"Perturbation (astronomy)","score":0.4510999917984009},{"id":"https://openalex.org/keywords/perturbation-theory","display_name":"Perturbation theory (quantum mechanics)","score":0.38850000500679016},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.35530000925064087},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.3440000116825104}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6219000220298767},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6190000176429749},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5964999794960022},{"id":"https://openalex.org/C162641036","wikidata":"https://www.wikidata.org/wiki/Q5500215","display_name":"Free energy perturbation","level":3,"score":0.5898000001907349},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.487199991941452},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.4830999970436096},{"id":"https://openalex.org/C177918212","wikidata":"https://www.wikidata.org/wiki/Q803623","display_name":"Perturbation (astronomy)","level":2,"score":0.4510999917984009},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3937999904155731},{"id":"https://openalex.org/C174256460","wikidata":"https://www.wikidata.org/wiki/Q911364","display_name":"Perturbation theory (quantum mechanics)","level":2,"score":0.38850000500679016},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.38839998841285706},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3856000006198883},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37720000743865967},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.35530000925064087},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3440000116825104},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.34380000829696655},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.3434999883174896},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.3395000100135803},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.3352000117301941},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.3206000030040741},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.30959999561309814},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.30630001425743103},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2847000062465668},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.2743000090122223},{"id":"https://openalex.org/C127964446","wikidata":"https://www.wikidata.org/wiki/Q1092142","display_name":"Computational resource","level":3,"score":0.267300009727478},{"id":"https://openalex.org/C62354387","wikidata":"https://www.wikidata.org/wiki/Q875399","display_name":"Boundary (topology)","level":2,"score":0.2671999931335449},{"id":"https://openalex.org/C84551667","wikidata":"https://www.wikidata.org/wiki/Q155640","display_name":"Potential energy","level":2,"score":0.2506999969482422},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25060001015663147}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"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":"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":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1021/acs.jcim.5c02932","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02932","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02932?ref=article_openPDF","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:41685578","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41685578","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:digital.csic.es:10261/434829","is_oa":true,"landing_page_url":"http://hdl.handle.net/10261/434829","pdf_url":null,"source":{"id":"https://openalex.org/S4306401639","display_name":"DIGITAL.CSIC (Spanish National Research Council (CSIC))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I134820265","host_organization_name":"Consejo Superior de Investigaciones Cient\u00edficas","host_organization_lineage":["https://openalex.org/I134820265"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:DiVA.org:uu-589159","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-589159","pdf_url":null,"source":{"id":"https://openalex.org/S4306402043","display_name":"Uppsala University Publications (Uppsala University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123387679","host_organization_name":"Uppsala University","host_organization_lineage":["https://openalex.org/I123387679"],"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":null,"raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:13014454","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13014454/","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,"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":"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.5c02932","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02932","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c02932?ref=article_openPDF","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":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.6082532405853271}],"awards":[{"id":"https://openalex.org/G2362151103","display_name":null,"funder_award_id":"2023.0210","funder_id":"https://openalex.org/F4320322327","funder_display_name":"Knut och Alice Wallenbergs Stiftelse"},{"id":"https://openalex.org/G3197889401","display_name":"Drug repurposing and discovery multidisciplinary training network","funder_award_id":"955879","funder_id":"https://openalex.org/F4320338337","funder_display_name":"H2020 Marie Sk\u0142odowska-Curie Actions"},{"id":"https://openalex.org/G4914628656","display_name":null,"funder_award_id":"2022-03441","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"},{"id":"https://openalex.org/G5462394322","display_name":"Novel Oncological Targets - Inhibiting Cancer via Mutated G Proteins","funder_award_id":"VI.Veni.232.243","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G7672583514","display_name":null,"funder_award_id":"PID2023- 150793OB-I00","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"}],"funders":[{"id":"https://openalex.org/F4320315062","display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades","ror":null},{"id":"https://openalex.org/F4320320929","display_name":"Universiteit Leiden","ror":"https://ror.org/027bh9e22"},{"id":"https://openalex.org/F4320321799","display_name":"Ministerie van Onderwijs, Cultuur en Wetenschap","ror":"https://ror.org/02x3w5g21"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"},{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320323823","display_name":"Universidad de Oviedo","ror":"https://ror.org/006gksa02"},{"id":"https://openalex.org/F4320324119","display_name":"Uppsala Universitet","ror":"https://ror.org/048a87296"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320338337","display_name":"H2020 Marie Sk\u0142odowska-Curie Actions","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7128843748.pdf","grobid_xml":"https://content.openalex.org/works/W7128843748.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1974167806","https://openalex.org/W1976499671","https://openalex.org/W1982680156","https://openalex.org/W1984261657","https://openalex.org/W2025006523","https://openalex.org/W2037535298","https://openalex.org/W2044656372","https://openalex.org/W2140047797","https://openalex.org/W2140151763","https://openalex.org/W2151020862","https://openalex.org/W2154670681","https://openalex.org/W2161605421","https://openalex.org/W2222589778","https://openalex.org/W2404280981","https://openalex.org/W2587480998","https://openalex.org/W2597025763","https://openalex.org/W2749873612","https://openalex.org/W2772606519","https://openalex.org/W2898021236","https://openalex.org/W2912818999","https://openalex.org/W2941138866","https://openalex.org/W2990010612","https://openalex.org/W3047663514","https://openalex.org/W3054319032","https://openalex.org/W3098306447","https://openalex.org/W4297914802","https://openalex.org/W4376226284","https://openalex.org/W4386245738","https://openalex.org/W4391637501","https://openalex.org/W4399347516","https://openalex.org/W4403099221","https://openalex.org/W4410974264","https://openalex.org/W6892699366","https://openalex.org/W6950322510","https://openalex.org/W7084395135","https://openalex.org/W7115913794"],"related_works":[],"abstract_inverted_index":{"Predicting":[0],"how":[1],"chemical":[2,90],"modifications":[3],"affect":[4],"drug":[5,11,196],"binding":[6,23,56,78,200],"is":[7],"central":[8],"to":[9,72,122,209],"rational":[10],"design.":[12],"Free":[13],"energy":[14],"perturbation":[15,138,144],"(FEP)":[16],"calculations":[17],"provide":[18],"accurate":[19],"estimates":[20],"of":[21,133,179],"these":[22],"affinity":[24,201],"changes,":[25],"but":[26],"existing":[27],"methods":[28],"often":[29],"require":[30],"substantial":[31],"computational":[32,135,156,163,183,214],"resources":[33],"and":[34,50,95,110,125,146,182,208],"expert":[35],"knowledge.":[36],"Here,":[37],"we":[38],"present":[39],"QligFEP":[40,80,118,186],"v2.1.0,":[41],"a":[42,48,73,82,131,188],"flexible":[43],"open-source":[44,126],"workflow":[45],"based":[46],"on":[47,154,172],"graphical":[49],"command-line":[51],"interface":[52],"for":[53,168,191,204],"calculating":[54],"relative":[55],"free":[57],"energies":[58],"using":[59,103],"spherical":[60],"boundary":[61],"conditions,":[62],"which":[63],"dramatically":[64],"reduces":[65],"simulation":[66],"system":[67],"size":[68],"by":[69],"confining":[70],"simulations":[71],"focused":[74],"region":[75],"around":[76],"the":[77,101,134],"site.":[79],"features":[81],"configurable":[83],"restraint":[84],"algorithm":[85],"that":[86,117],"automatically":[87],"handles":[88],"diverse":[89],"transformations,":[91],"streamlined":[92],"setup":[93],"procedures,":[94],"enhanced":[96],"analysis":[97,115],"tools.":[98],"We":[99],"validated":[100],"method":[102],"industry":[104],"benchmarks":[105],"comprising":[106],"16":[107],"protein":[108],"targets":[109],"639":[111],"ligand":[112],"transformations.":[113],"Statistical":[114],"demonstrates":[116],"achieves":[119],"comparable":[120],"accuracy":[121],"established":[123],"commercial":[124],"alternatives":[127],"while":[128],"requiring":[129],"only":[130],"fraction":[132],"resources.":[136],"The":[137,177],"protocol":[139],"simulates":[140],"\u223c6250":[141],"atoms":[142],"per":[143],"leg":[145],"completes":[147],"transformation":[148],"replicates":[149],"in":[150,195],"under":[151],"2":[152],"h":[153],"standard":[155],"clusters.":[157],"Unlike":[158],"full-system":[159],"simulations,":[160],"QligFEP's":[161],"modest":[162],"requirements":[164],"make":[165],"FEP":[166],"accessible":[167,203],"less":[169],"than":[170],"$1":[171],"current":[173],"AWS":[174],"spot":[175],"instances.":[176],"combination":[178],"accuracy,":[180],"flexibility,":[181],"efficiency":[184],"positions":[185],"as":[187],"practical":[189],"solution":[190],"accelerating":[192],"compound":[193],"optimization":[194],"discovery,":[197],"making":[198],"rigorous":[199],"predictions":[202],"large":[205],"scale":[206],"applications":[207],"research":[210],"groups":[211],"with":[212],"limited":[213],"infrastructure.":[215]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2026-02-14T00:00:00"}
