{"id":"https://openalex.org/W7134831398","doi":"https://doi.org/10.1021/acs.jcim.6c00528","title":"Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization","display_name":"Automated Force Field Developer and Optimizer Platform: Torsion Reparameterization","publication_year":2026,"publication_date":"2026-03-09","ids":{"openalex":"https://openalex.org/W7134831398","doi":"https://doi.org/10.1021/acs.jcim.6c00528","pmid":"https://pubmed.ncbi.nlm.nih.gov/41802224"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6c00528","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c00528","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.6c00528","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027909348","display_name":"Alejandro Blanco-Gonz\u00e1lez","orcid":"https://orcid.org/0000-0001-7379-2588"},"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":"Alejandro Blanco-Gonzalez","raw_affiliation_strings":["ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States"],"raw_orcid":"https://orcid.org/0000-0001-7379-2588","affiliations":[{"raw_affiliation_string":"ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029318245","display_name":"William Betancourt","orcid":null},"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":"William Betancourt","raw_affiliation_strings":["Department of Computer Science and Engineering","Michigan State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Michigan State University","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128652711","display_name":"Ryan Michael Snyder","orcid":null},"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/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP","NL"],"is_corresponding":false,"raw_author_name":"Ryan Michael Snyder","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology","Rutgers University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053912177","display_name":"S. Zhang","orcid":null},"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/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP","NL"],"is_corresponding":false,"raw_author_name":"Shi Zhang","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research 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, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]},{"author_position":"middle","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/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP","NL"],"is_corresponding":false,"raw_author_name":"Timothy J. Giese","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research 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, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210150921"]},{"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/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]}],"countries":["JP","NL"],"is_corresponding":false,"raw_author_name":"Zeke A. Piskulich","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research 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, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112716265","display_name":"Andreas W. G\u00f6tz","orcid":null},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]},{"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/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":true,"raw_author_name":"Andreas W. G\u00f6tz","raw_affiliation_strings":["ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States","San Diego Supercomputer Center","University of California San Diego"],"raw_orcid":"https://orcid.org/0000-0002-8048-6906","affiliations":[{"raw_affiliation_string":"ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"San Diego Supercomputer Center","institution_ids":["https://openalex.org/I181653535"]},{"raw_affiliation_string":"University of California San Diego","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085994852","display_name":"Kenneth M. Merz","orcid":"https://orcid.org/0000-0001-9139-5893"},"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":true,"raw_author_name":"Kenneth M. Merz","raw_affiliation_strings":["ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States","Department of Chemistry and Department of Biochemistry and Molecular Biology","Michigan State University"],"raw_orcid":"https://orcid.org/0000-0001-9139-5893","affiliations":[{"raw_affiliation_string":"ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Chemistry and Department of Biochemistry and Molecular Biology","institution_ids":[]},{"raw_affiliation_string":"Michigan State University","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","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/I4210150921","display_name":"RIKEN Center for Integrative Medical Sciences","ror":"https://ror.org/04mb6s476","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210150921"]},{"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":["JP","NL","US"],"is_corresponding":true,"raw_author_name":"Darrin M. York","raw_affiliation_strings":["ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States","Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology","Rutgers University"],"raw_orcid":"https://orcid.org/0000-0002-9193-7055","affiliations":[{"raw_affiliation_string":"ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology","institution_ids":["https://openalex.org/I4210150921"]},{"raw_affiliation_string":"Rutgers University","institution_ids":["https://openalex.org/I4210096112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072718512","display_name":"Hasan Metin Aktulga","orcid":"https://orcid.org/0000-0003-3061-6378"},"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":true,"raw_author_name":"Hasan Metin Aktulga","raw_affiliation_strings":["ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States","Department of Computer Science and Engineering","Michigan State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"Department of Computer Science and Engineering","institution_ids":[]},{"raw_affiliation_string":"Michigan State University","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077927177","display_name":"Madushanka Manathunga","orcid":"https://orcid.org/0000-0002-3594-8112"},"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":true,"raw_author_name":"Madushanka Manathunga","raw_affiliation_strings":["ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States"],"raw_orcid":"https://orcid.org/0000-0002-3594-8112","affiliations":[{"raw_affiliation_string":"ATTMOS Inc., 325 E Grand River Ave Ste 328, East Lansing, Michigan 48823, United States","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5072718512","https://openalex.org/A5076436548","https://openalex.org/A5077927177","https://openalex.org/A5085994852","https://openalex.org/A5112716265"],"corresponding_institution_ids":["https://openalex.org/I181653535","https://openalex.org/I36258959","https://openalex.org/I4210096112","https://openalex.org/I4210150921","https://openalex.org/I87216513"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.39467793,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"6","first_page":"3206","last_page":"3219"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5200999975204468,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.5200999975204468,"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":0.17659999430179596,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.039000000804662704,"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/torsion","display_name":"Torsion (gastropod)","score":0.8414000272750854},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.6875},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.3628000020980835},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.3303000032901764},{"id":"https://openalex.org/keywords/potential-energy","display_name":"Potential energy","score":0.32600000500679016},{"id":"https://openalex.org/keywords/scaling","display_name":"Scaling","score":0.30820000171661377}],"concepts":[{"id":"https://openalex.org/C77461463","wikidata":"https://www.wikidata.org/wiki/Q7827201","display_name":"Torsion (gastropod)","level":2,"score":0.8414000272750854},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.6875},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5228999853134155},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4000000059604645},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.3628000020980835},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.33149999380111694},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.3303000032901764},{"id":"https://openalex.org/C84551667","wikidata":"https://www.wikidata.org/wiki/Q155640","display_name":"Potential energy","level":2,"score":0.32600000500679016},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.30979999899864197},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.30820000171661377},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3068999946117401},{"id":"https://openalex.org/C201194858","wikidata":"https://www.wikidata.org/wiki/Q898238","display_name":"Steric effects","level":2,"score":0.3034000098705292},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.29429998993873596},{"id":"https://openalex.org/C3767888","wikidata":"https://www.wikidata.org/wiki/Q4117184","display_name":"Force density","level":2,"score":0.2825999855995178},{"id":"https://openalex.org/C57614664","wikidata":"https://www.wikidata.org/wiki/Q27037480","display_name":"Torsion spring","level":2,"score":0.27869999408721924},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.27079999446868896},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.262800008058548},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2599000036716461}],"mesh":[{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001331","descriptor_name":"Automation","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":"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":"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":"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":"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":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","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},{"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.6c00528","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c00528","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:41802224","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41802224","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:13014461","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13014461/","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.6c00528","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6c00528","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":0.7921095490455627}],"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/G3628703512","display_name":null,"funder_award_id":"R01GM130641","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3669847442","display_name":null,"funder_award_id":"R44GM150347","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4499646989","display_name":null,"funder_award_id":"2435622","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6335681527","display_name":null,"funder_award_id":"2209717","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"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":66,"referenced_works":["https://openalex.org/W1976161355","https://openalex.org/W1981745234","https://openalex.org/W1982703140","https://openalex.org/W1989793475","https://openalex.org/W2000359198","https://openalex.org/W2004822259","https://openalex.org/W2008423326","https://openalex.org/W2015688756","https://openalex.org/W2024726841","https://openalex.org/W2027408247","https://openalex.org/W2035199159","https://openalex.org/W2037535298","https://openalex.org/W2041189078","https://openalex.org/W2043628797","https://openalex.org/W2051669046","https://openalex.org/W2052559859","https://openalex.org/W2052573265","https://openalex.org/W2067174909","https://openalex.org/W2072683434","https://openalex.org/W2111917512","https://openalex.org/W2122199548","https://openalex.org/W2147993766","https://openalex.org/W2150789776","https://openalex.org/W2154670681","https://openalex.org/W2244785476","https://openalex.org/W2313116527","https://openalex.org/W2323616528","https://openalex.org/W2344252179","https://openalex.org/W2540491215","https://openalex.org/W2541404351","https://openalex.org/W2891791233","https://openalex.org/W2911997094","https://openalex.org/W2912818999","https://openalex.org/W2914938805","https://openalex.org/W2962729078","https://openalex.org/W2974163880","https://openalex.org/W2989052455","https://openalex.org/W3003257820","https://openalex.org/W3033054884","https://openalex.org/W3034390843","https://openalex.org/W3048565185","https://openalex.org/W3086801715","https://openalex.org/W3109230444","https://openalex.org/W3138127219","https://openalex.org/W3164526122","https://openalex.org/W3182915053","https://openalex.org/W4206277361","https://openalex.org/W4284709266","https://openalex.org/W4285331314","https://openalex.org/W4308653706","https://openalex.org/W4310573576","https://openalex.org/W4315631931","https://openalex.org/W4318035807","https://openalex.org/W4318692572","https://openalex.org/W4376226284","https://openalex.org/W4387334097","https://openalex.org/W4387440676","https://openalex.org/W4387865192","https://openalex.org/W4395677718","https://openalex.org/W4396561721","https://openalex.org/W4399880623","https://openalex.org/W4402206730","https://openalex.org/W4408914802","https://openalex.org/W4409826630","https://openalex.org/W4410567690","https://openalex.org/W4412727004"],"related_works":[],"abstract_inverted_index":{"General":[0,5],"force":[1,30],"fields":[2],"such":[3],"as":[4],"Amber":[6],"Force":[7,81],"Field":[8,82],"(GAFF)":[9],"have":[10],"been":[11],"designed":[12],"for":[13,46,56,96],"broad":[14],"applicability":[15],"and":[16,40,65,74,84,120,143],"are":[17,33,60],"widely":[18],"used":[19],"in":[20,24,169],"protein-ligand":[21,146],"binding":[22,48,148],"simulations":[23],"structure-based":[25],"drug":[26],"discovery.":[27],"However,":[28],"the":[29,79,105],"field":[31],"parameters":[32,95,163],"not":[34],"always":[35],"transferable":[36],"across":[37],"ligand":[38],"molecules,":[39],"custom":[41],"reparameterization":[42],"is":[43,53],"sometimes":[44],"necessary":[45],"accurate":[47],"free":[49,149],"energy":[50,150],"simulations.":[51,152],"This":[52],"especially":[54],"true":[55],"torsion":[57,94,122,162],"parameters,":[58],"which":[59,168],"highly":[61],"dependent":[62],"on":[63],"stereoelectronic":[64],"steric":[66],"effects.":[67],"Here,":[68],"we":[69],"report":[70],"a":[71,100,125,138,181],"novel,":[72],"flexible,":[73],"user-friendly":[75],"computational":[76,183],"tool":[77],"called":[78],"Automated":[80],"Developer":[83],"Optimizer":[85],"(AFFDO)":[86],"platform":[87],"that":[88,129,156],"allows":[89],"generating":[90],"accurate,":[91],"tailored":[92],"GAFF2":[93,161],"drug-like":[97,141],"molecules.":[98],"For":[99],"given":[101],"ligand,":[102],"AFFDO":[103,135,157],"selects":[104],"most":[106],"important":[107],"torsions,":[108],"carries":[109],"out":[110,145],"GPU-accelerated":[111],"density":[112],"functional":[113],"theory":[114],"calculations":[115],"to":[116],"collect":[117],"reference":[118,166],"data":[119],"fits":[121],"terms":[123],"using":[124],"fast":[126],"gradient-based":[127],"optimizer":[128],"leverages":[130],"automated":[131],"differentiation.":[132],"We":[133],"benchmark":[134],"by":[136],"parametrizing":[137],"series":[139],"of":[140],"molecules":[142],"carrying":[144],"relative":[147],"(RBFE)":[151],"The":[153],"results":[154],"show":[155],"can":[158],"significantly":[159],"improve":[160],"against":[164],"QM":[165],"data,":[167],"some":[170],"cases":[171],"translates":[172],"into":[173],"better":[174],"agreement":[175],"with":[176],"experimental":[177],"RBFE":[178],"values":[179],"within":[180],"reasonable":[182],"time.":[184]},"counts_by_year":[],"updated_date":"2026-05-21T09:19:25.381259","created_date":"2026-03-11T00:00:00"}