{"id":"https://openalex.org/W4389334468","doi":"https://doi.org/10.1021/acs.jcim.3c01513","title":"Polarizable AMOEBA Model for Simulating Mg 2+ \u00b7Protein\u00b7Nucleotide Complexes","display_name":"Polarizable AMOEBA Model for Simulating Mg 2+ \u00b7Protein\u00b7Nucleotide Complexes","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4389334468","doi":"https://doi.org/10.1021/acs.jcim.3c01513","pmid":"https://pubmed.ncbi.nlm.nih.gov/38051630"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01513","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01513","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,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-2"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6509d316ed7d0eccc3d54f6d/original/polarizable-amoeba-model-for-simulating-mg2-protein-nucleotide-complexes.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065912302","display_name":"Juli\u00e1n M. Delgado","orcid":"https://orcid.org/0000-0002-2304-8643","observed_orcids":["https://orcid.org/0000-0002-2304-8643"]},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julian M. Delgado","raw_affiliation_strings":["Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States"],"raw_orcid":"https://orcid.org/0000-0002-2304-8643","affiliations":[{"raw_affiliation_string":"Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States","institution_ids":["https://openalex.org/I2613432"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066613616","display_name":"P\u00e9ter R. Nagy","orcid":"https://orcid.org/0000-0001-6692-0879","observed_orcids":["https://orcid.org/0000-0001-6692-0879"]},"institutions":[{"id":"https://openalex.org/I29770179","display_name":"Budapest University of Technology and Economics","ror":"https://ror.org/02w42ss30","country_code":"HU","type":"education","lineage":["https://openalex.org/I29770179"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"P\u00e9ter R. Nagy","raw_affiliation_strings":["Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, M\u0171egyetem rkp. 3., Budapest H-1111, Hungary","HUN-REN-BME Quantum Chemistry Research Group, M\u0171egyetem rkp. 3., Budapest H-1111, Hungary","MTA-BME Lend\u00fclet Quantum Chemistry Research Group, M\u0171egyetem rkp. 3., Budapest H-1111, Hungary"],"raw_orcid":"https://orcid.org/0000-0001-6692-0879","affiliations":[{"raw_affiliation_string":"Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, M\u0171egyetem rkp. 3., Budapest H-1111, Hungary","institution_ids":["https://openalex.org/I29770179"]},{"raw_affiliation_string":"HUN-REN-BME Quantum Chemistry Research Group, M\u0171egyetem rkp. 3., Budapest H-1111, Hungary","institution_ids":["https://openalex.org/I29770179"]},{"raw_affiliation_string":"MTA-BME Lend\u00fclet Quantum Chemistry Research Group, M\u0171egyetem rkp. 3., Budapest H-1111, Hungary","institution_ids":["https://openalex.org/I29770179"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004495836","display_name":"Sameer Varma","orcid":"https://orcid.org/0000-0002-7827-5632","observed_orcids":["https://orcid.org/0000-0002-7827-5632"]},"institutions":[{"id":"https://openalex.org/I2613432","display_name":"University of South Florida","ror":"https://ror.org/032db5x82","country_code":"US","type":"education","lineage":["https://openalex.org/I2613432"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sameer Varma","raw_affiliation_strings":["Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States","Department of Physics, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States"],"raw_orcid":"https://orcid.org/0000-0002-7827-5632","affiliations":[{"raw_affiliation_string":"Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States","institution_ids":["https://openalex.org/I2613432"]},{"raw_affiliation_string":"Department of Physics, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States","institution_ids":["https://openalex.org/I2613432"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5004495836"],"corresponding_institution_ids":["https://openalex.org/I2613432"],"apc_list":{"value":5000,"currency":"USD","value_usd":5000},"apc_paid":null,"fwci":0.979,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.73124727,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"64","issue":"2","first_page":"378","last_page":"392"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.701200008392334,"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":0.701200008392334,"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/T10002","display_name":"Advanced Chemical Physics Studies","score":0.27149999141693115,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.01489999983459711,"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/polarizable-force-field","display_name":"polarizable force field","score":0.781000018119812},{"id":"https://openalex.org/keywords/amoeba","display_name":"amoebae","score":0.9359999895095825},{"id":"https://openalex.org/keywords/divalent-cation-binding","display_name":"divalent cation binding","score":0.8029999732971191},{"id":"https://openalex.org/keywords/magnesium-ions","display_name":"magnesium ions","score":0.42100000381469727},{"id":"https://openalex.org/keywords/induced-dipoles","display_name":"induced dipoles","score":0.8550000190734863},{"id":"https://openalex.org/keywords/enzyme-catalysis","display_name":"enzyme catalysis","score":0.4740000069141388},{"id":"https://openalex.org/keywords/binding-free-energy","display_name":"binding free energy","score":0.6980000138282776},{"id":"https://openalex.org/keywords/molecular-dynamics-simulation","display_name":"molecular dynamics simulation","score":0.3529999852180481}],"concepts":[{"id":"https://openalex.org/C74884574","wikidata":"https://www.wikidata.org/wiki/Q171407","display_name":"Divalent","level":2,"score":0.6576047539710999},{"id":"https://openalex.org/C139287275","wikidata":"https://www.wikidata.org/wiki/Q869891","display_name":"Polarizability","level":3,"score":0.6574419736862183},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6105824708938599},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.5630103349685669},{"id":"https://openalex.org/C119049451","wikidata":"https://www.wikidata.org/wiki/Q3318070","display_name":"Water model","level":3,"score":0.43826109170913696},{"id":"https://openalex.org/C173523689","wikidata":"https://www.wikidata.org/wiki/Q215589","display_name":"Dipole","level":2,"score":0.42275992035865784},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.403409868478775},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.3932728171348572},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3397899866104126},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3266335725784302},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.1593940556049347},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.10951915383338928},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000255","descriptor_name":"Adenosine Triphosphate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000656","descriptor_name":"Amoeba","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000656","descriptor_name":"Amoeba","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000656","descriptor_name":"Amoeba","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000656","descriptor_name":"Amoeba","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000656","descriptor_name":"Amoeba","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000656","descriptor_name":"Amoeba","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000656","descriptor_name":"Amoeba","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002413","descriptor_name":"Cations, Divalent","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002413","descriptor_name":"Cations, Divalent","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002413","descriptor_name":"Cations, Divalent","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002413","descriptor_name":"Cations, Divalent","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002413","descriptor_name":"Cations, Divalent","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002413","descriptor_name":"Cations, Divalent","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002413","descriptor_name":"Cations, Divalent","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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":"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},{"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":5,"locations":[{"id":"doi:10.1021/acs.jcim.3c01513","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01513","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,"listed_in":["cwts-core","jufo-1","ki-jl-1","medline","norway-2"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"doi:10.26434/chemrxiv-2023-bvndw","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv-2023-bvndw","pdf_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6509d316ed7d0eccc3d54f6d/original/polarizable-amoeba-model-for-simulating-mg2-protein-nucleotide-complexes.pdf","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},{"id":"pmid:38051630","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38051630","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":"Journal Article"},{"id":"pmh:oai:real.mtak.hu:205923","is_oa":false,"landing_page_url":"https://real.mtak.hu/205923/1/polarizable-amoeba-model-for-simulating-mg2-protein-nucleotide-complexes.pdf","pdf_url":"https://real.mtak.hu/205923/1/polarizable-amoeba-model-for-simulating-mg2-protein-nucleotide-complexes.pdf","source":{"id":"https://openalex.org/S4306400081","display_name":"Repository of the Academy's Library (Library of the Hungarian Academy of Sciences)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210140733","host_organization_name":"Library and Information Centre of the Hungarian Academy of Sciences","host_organization_lineage":["https://openalex.org/I4210140733"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11345861","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11345861","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11345861/pdf/nihms-2014261.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.26434/chemrxiv-2023-bvndw","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv-2023-bvndw","pdf_url":"https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6509d316ed7d0eccc3d54f6d/original/polarizable-amoeba-model-for-simulating-mg2-protein-nucleotide-complexes.pdf","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"score":0.7200000286102295,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1126814021","display_name":null,"funder_award_id":"101076972","funder_id":"https://openalex.org/F4320334678","funder_display_name":"European Research Council"},{"id":"https://openalex.org/G2805387630","display_name":"Turning gold standard quantum chemistry into a routine simulation tool: predictive properties for large molecular systems","funder_award_id":"101076972","funder_id":"https://openalex.org/F4320338453","funder_display_name":"HORIZON EUROPE European Research Council"},{"id":"https://openalex.org/G4584483396","display_name":null,"funder_award_id":"FK142489","funder_id":"https://openalex.org/F4320336675","funder_display_name":"National Research, Development and Innovation Office"},{"id":"https://openalex.org/G712350737","display_name":null,"funder_award_id":"R01 GM147210","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8207839096","display_name":null,"funder_award_id":"KKP126451","funder_id":"https://openalex.org/F4320336675","funder_display_name":"National Research, Development and Innovation Office"},{"id":"https://openalex.org/G8629050340","display_name":null,"funder_award_id":"R01 GM118697","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320322192","display_name":"Magyar Tudom\u00e1nyos Akad\u00e9mia","ror":"https://ror.org/02ks8qq67"},{"id":"https://openalex.org/F4320334678","display_name":"European Research Council","ror":"https://ror.org/0472cxd90"},{"id":"https://openalex.org/F4320336675","display_name":"National Research, Development and Innovation Office","ror":null},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320338453","display_name":"HORIZON EUROPE European Research Council","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4389334468.pdf","grobid_xml":"https://content.openalex.org/works/W4389334468.grobid-xml"},"referenced_works_count":115,"referenced_works":["https://openalex.org/W102942757","https://openalex.org/W153460014","https://openalex.org/W243911733","https://openalex.org/W1501596101","https://openalex.org/W1502531368","https://openalex.org/W1563380435","https://openalex.org/W1665040566","https://openalex.org/W1963989486","https://openalex.org/W1967737979","https://openalex.org/W1968757798","https://openalex.org/W1971162911","https://openalex.org/W1978189250","https://openalex.org/W1979401635","https://openalex.org/W1981368803","https://openalex.org/W1986709960","https://openalex.org/W1987178045","https://openalex.org/W1987981639","https://openalex.org/W1988543095","https://openalex.org/W1991667171","https://openalex.org/W1992531741","https://openalex.org/W2001069120","https://openalex.org/W2002782616","https://openalex.org/W2003157811","https://openalex.org/W2003182537","https://openalex.org/W2006183679","https://openalex.org/W2008423326","https://openalex.org/W2016059492","https://openalex.org/W2017829285","https://openalex.org/W2017835622","https://openalex.org/W2020618854","https://openalex.org/W2021088564","https://openalex.org/W2021799030","https://openalex.org/W2023826882","https://openalex.org/W2024786978","https://openalex.org/W2025131154","https://openalex.org/W2031674868","https://openalex.org/W2032642369","https://openalex.org/W2035012908","https://openalex.org/W2035951662","https://openalex.org/W2039231719","https://openalex.org/W2041074466","https://openalex.org/W2041902442","https://openalex.org/W2044940178","https://openalex.org/W2047399603","https://openalex.org/W2048454428","https://openalex.org/W2049764984","https://openalex.org/W2057477511","https://openalex.org/W2058538213","https://openalex.org/W2059885388","https://openalex.org/W2060366601","https://openalex.org/W2063119861","https://openalex.org/W2065283382","https://openalex.org/W2067076385","https://openalex.org/W2069006374","https://openalex.org/W2069750852","https://openalex.org/W2073515932","https://openalex.org/W2075093176","https://openalex.org/W2077096083","https://openalex.org/W2077501220","https://openalex.org/W2079666836","https://openalex.org/W2080042107","https://openalex.org/W2089745310","https://openalex.org/W2114003088","https://openalex.org/W2122199548","https://openalex.org/W2125199093","https://openalex.org/W2140151763","https://openalex.org/W2144288821","https://openalex.org/W2148424525","https://openalex.org/W2155836103","https://openalex.org/W2159010139","https://openalex.org/W2166201936","https://openalex.org/W2169834283","https://openalex.org/W2169892960","https://openalex.org/W2171047927","https://openalex.org/W2203816174","https://openalex.org/W2316392160","https://openalex.org/W2322200946","https://openalex.org/W2324930475","https://openalex.org/W2337762266","https://openalex.org/W2339992943","https://openalex.org/W2411580022","https://openalex.org/W2439255672","https://openalex.org/W2489958357","https://openalex.org/W2588001619","https://openalex.org/W2613115649","https://openalex.org/W2621161140","https://openalex.org/W2766682498","https://openalex.org/W2793701070","https://openalex.org/W2810062942","https://openalex.org/W2906336610","https://openalex.org/W2918768857","https://openalex.org/W2923759574","https://openalex.org/W2949150302","https://openalex.org/W2970397043","https://openalex.org/W2990752114","https://openalex.org/W2992305306","https://openalex.org/W3006671424","https://openalex.org/W3008495456","https://openalex.org/W3081427668","https://openalex.org/W3083637251","https://openalex.org/W3086059121","https://openalex.org/W3104031547","https://openalex.org/W3111232582","https://openalex.org/W3129376431","https://openalex.org/W3137242203","https://openalex.org/W3152978999","https://openalex.org/W3162615688","https://openalex.org/W4205246014","https://openalex.org/W4213452100","https://openalex.org/W4233253307","https://openalex.org/W4252222576","https://openalex.org/W4252474431","https://openalex.org/W4253191544","https://openalex.org/W4297965475","https://openalex.org/W6740664730"],"related_works":["https://openalex.org/W1998656087","https://openalex.org/W2107075767","https://openalex.org/W2175138132","https://openalex.org/W1978989175","https://openalex.org/W2085356040","https://openalex.org/W2954518162","https://openalex.org/W2110300847","https://openalex.org/W2132480759","https://openalex.org/W2077731080","https://openalex.org/W2323458937"],"abstract_inverted_index":{"Molecular":[0],"mechanics":[1],"(MM)":[2],"simulations":[3,45,273],"have":[4],"the":[5,12,24,31,67,86,111,139,171,253],"potential":[6],"to":[7,36,92,150,165,185,190,201,227,283],"provide":[8,106],"detailed":[9],"insights":[10,259],"into":[11,260],"mechanisms":[13],"of":[14,26,33,52,69,78,88,110,138,174,178,221,274],"enzymes":[15,28],"that":[16,119,134,206,269],"utilize":[17],"nucleotides":[18],"as":[19,129,234,236],"cofactors.":[20],"In":[21],"most":[22],"cases,":[23],"activities":[25],"these":[27,89,102,280],"also":[29,216],"require":[30],"binding":[32,249],"divalent":[34,41,79],"cations":[35,42,80],"catalytic":[37,291],"sites.":[38],"However,":[39],"modeling":[40],"in":[43,75,252,287],"MM":[44],"has":[46],"been":[47],"chal-":[48],"lenging.":[49],"The":[50,176,195,242],"inclusion":[51,68,177],"explicit":[53],"polarization":[54,225],"was":[55],"considered":[56],"promising,":[57],"but":[58],"despite":[59,66],"improvements":[60,281],"over":[61],"non-polarizable":[62],"force":[63],"fields":[64],"and":[65,115,213,239,256,289,296],"\u2018Nonbonded-":[70],"fix":[71],"(NB-fix)\u2019":[72],"corrections,":[73],"errors":[74,161,196],"interaction":[76,156],"energies":[77],"with":[81,199,223,264,279],"proteins":[82],"remain":[83],"large.":[84],"Importantly,":[85],"application":[87],"models":[90],"fails":[91],"reproduce":[93],"experimental":[94,247],"structural":[95],"data":[96],"on":[97,101],"Mg2+\u00b7Protein\u00b7ATP":[98],"complexes.":[99],"Focusing":[100],"complexes,":[103],"here":[104],"we":[105,207,267],"a":[107,218,284],"systematic":[108],"assessment":[109],"polarizable":[112],"AMOEBA":[113,140],"model":[114,142,220,244],"recommend":[116],"critical":[117],"changes":[118],"substantially":[120],"improve":[121],"its":[122,230],"predictive":[123],"performance.":[124],"Our":[125],"key":[126],"results":[127],"are":[128,197],"follows.":[130],"We":[131,215],"first":[132],"show":[133,268],"our":[135],"recent":[136],"revision":[137],"protein":[141],"(AMOEBABIO18-HFC),":[143],"which":[144,188],"contains":[145],"high":[146,231],"field":[147,232],"corrections":[148,181],"(HFC)":[149],"induced":[151],"dipoles,":[152],"dramatically":[153],"improves":[154],"Mg2+-protein":[155],"energies,":[157],"reducing":[158],"mean":[159],"absolute":[160],"(MAE)":[162],"from":[163],"17":[164],"10":[166],"kcal/mol.":[167],"This":[168],"further":[169,182],"supports":[170],"general":[172],"applicability":[173],"AMOEBABIO18-HFC.":[175],"many-body":[179],"NB-fix":[180],"reduces":[183],"MAE":[184],"6":[186],"kcal/mol,":[187],"amounts":[189],"less":[191],"than":[192],"2%":[193],"error.":[194],"estimated":[198],"respect":[200],"vdW-inclusive":[202],"density":[203],"functional":[204],"theory":[205],"bench-":[208],"mark":[209],"against":[210],"CCSD(T)":[211],"calculations":[212],"experiments.":[214],"present":[217],"new":[219,237,258],"ATP":[222,243],"revised":[224],"parameters":[226],"better":[228,285],"capture":[229],"response,":[233],"well":[235],"vdW":[238],"dihedral":[240],"parameters.":[241],"accurately":[245],"predicts":[246],"Mg2+-ATP":[248],"free":[250],"energy":[251],"aqueous":[254],"phase":[255],"provides":[257],"how":[261],"Mg2+":[262],"associates":[263],"ATP.":[265],"Finally,":[266],"molecular":[270],"dynamics":[271],"(MD)":[272],"Mg2+\u00b7Kinase\u00b7ATP":[275],"complexes":[276],"carried":[277],"out":[278],"lead":[282],"agreement":[286],"global":[288],"local":[290],"site":[292],"structures":[293],"between":[294],"MD":[295],"X-ray":[297],"crystallography.":[298]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2026-10-08T09:06:37.294493","created_date":"2023-12-06T00:00:00"}