{"id":"https://openalex.org/W4297965475","doi":"https://doi.org/10.1021/acs.jcim.2c00758","title":"Inclusion of High-Field Target Data in AMOEBA\u2019s Calibration Improves Predictions of Protein\u2013Ion Interactions","display_name":"Inclusion of High-Field Target Data in AMOEBA\u2019s Calibration Improves Predictions of Protein\u2013Ion Interactions","publication_year":2022,"publication_date":"2022-09-29","ids":{"openalex":"https://openalex.org/W4297965475","doi":"https://doi.org/10.1021/acs.jcim.2c00758","pmid":"https://pubmed.ncbi.nlm.nih.gov/36173398"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c00758","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00758","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":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://www.ncbi.nlm.nih.gov/pmc/articles/9817009","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020734148","display_name":"Juli\u00e1n A. Delgado","orcid":null},"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":"Juli\u00e1n A. Delgado","raw_affiliation_strings":["Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States"],"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Microbiology and Molecular Biology, 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/A5035755950","display_name":"Vered Wineman\u2010Fisher","orcid":"https://orcid.org/0000-0002-5124-5900"},"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":"Vered Wineman-Fisher","raw_affiliation_strings":["Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States"],"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Microbiology and Molecular Biology, 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/A5102932940","display_name":"Sagar A. Pandit","orcid":"https://orcid.org/0000-0002-7728-9477"},"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":"Sagar Pandit","raw_affiliation_strings":["Department of Physics, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States"],"affiliations":[{"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"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004495836","display_name":"Sameer Varma","orcid":"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 Cell Biology, Microbiology and Molecular Biology, 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"],"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Microbiology and Molecular Biology, 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":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5004495836"],"corresponding_institution_ids":["https://openalex.org/I2613432"],"apc_list":null,"apc_paid":null,"fwci":1.6418,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.83508251,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"62","issue":"19","first_page":"4713","last_page":"4726"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T11177","display_name":"Spectroscopy and Quantum Chemical Studies","score":0.9995999932289124,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9966999888420105,"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/polarizability","display_name":"Polarizability","score":0.819884181022644},{"id":"https://openalex.org/keywords/ion","display_name":"Ion","score":0.7288549542427063},{"id":"https://openalex.org/keywords/van-der-waals-force","display_name":"van der Waals force","score":0.6690950393676758},{"id":"https://openalex.org/keywords/water-model","display_name":"Water model","score":0.601812481880188},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5930593013763428},{"id":"https://openalex.org/keywords/force-field","display_name":"Force field (fiction)","score":0.5703727006912231},{"id":"https://openalex.org/keywords/electrostatics","display_name":"Electrostatics","score":0.5061261057853699},{"id":"https://openalex.org/keywords/potential-of-mean-force","display_name":"Potential of mean force","score":0.4727776050567627},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.46939510107040405},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4377455711364746},{"id":"https://openalex.org/keywords/chemical-physics","display_name":"Chemical physics","score":0.4264352023601532},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3435021638870239},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.3402271866798401},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3348519206047058},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.24086284637451172},{"id":"https://openalex.org/keywords/physical-chemistry","display_name":"Physical chemistry","score":0.15517809987068176},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.15298283100128174}],"concepts":[{"id":"https://openalex.org/C139287275","wikidata":"https://www.wikidata.org/wiki/Q869891","display_name":"Polarizability","level":3,"score":0.819884181022644},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.7288549542427063},{"id":"https://openalex.org/C126061179","wikidata":"https://www.wikidata.org/wiki/Q189627","display_name":"van der Waals force","level":3,"score":0.6690950393676758},{"id":"https://openalex.org/C119049451","wikidata":"https://www.wikidata.org/wiki/Q3318070","display_name":"Water model","level":3,"score":0.601812481880188},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5930593013763428},{"id":"https://openalex.org/C10803110","wikidata":"https://www.wikidata.org/wiki/Q1341441","display_name":"Force field (fiction)","level":2,"score":0.5703727006912231},{"id":"https://openalex.org/C117626034","wikidata":"https://www.wikidata.org/wiki/Q26336","display_name":"Electrostatics","level":2,"score":0.5061261057853699},{"id":"https://openalex.org/C175634916","wikidata":"https://www.wikidata.org/wiki/Q17075777","display_name":"Potential of mean force","level":3,"score":0.4727776050567627},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.46939510107040405},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4377455711364746},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.4264352023601532},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3435021638870239},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3402271866798401},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3348519206047058},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.24086284637451172},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.15517809987068176},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.15298283100128174},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"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":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002138","descriptor_name":"Calibration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007477","descriptor_name":"Ions","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":"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":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.2c00758","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c00758","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":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":"pmid:36173398","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36173398","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:9817009","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9817009","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:9817009","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9817009","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[{"score":0.7599999904632568,"display_name":"Clean water and sanitation","id":"https://metadata.un.org/sdg/6"}],"awards":[{"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/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":99,"referenced_works":["https://openalex.org/W160102508","https://openalex.org/W233729598","https://openalex.org/W1677100306","https://openalex.org/W1963989486","https://openalex.org/W1976501806","https://openalex.org/W1977464370","https://openalex.org/W1978189250","https://openalex.org/W1978740922","https://openalex.org/W1980198495","https://openalex.org/W1981225934","https://openalex.org/W1981368803","https://openalex.org/W1986709960","https://openalex.org/W1987178045","https://openalex.org/W1987981639","https://openalex.org/W1988127920","https://openalex.org/W1988543095","https://openalex.org/W1990513268","https://openalex.org/W1990719397","https://openalex.org/W1992212332","https://openalex.org/W1992531741","https://openalex.org/W2001443877","https://openalex.org/W2005420127","https://openalex.org/W2008423326","https://openalex.org/W2013836548","https://openalex.org/W2017835622","https://openalex.org/W2018940383","https://openalex.org/W2020618854","https://openalex.org/W2021799030","https://openalex.org/W2026741625","https://openalex.org/W2031674868","https://openalex.org/W2035012908","https://openalex.org/W2036042608","https://openalex.org/W2037487020","https://openalex.org/W2040809566","https://openalex.org/W2041074466","https://openalex.org/W2044828571","https://openalex.org/W2044940178","https://openalex.org/W2047493638","https://openalex.org/W2048094270","https://openalex.org/W2049764984","https://openalex.org/W2057089150","https://openalex.org/W2057216241","https://openalex.org/W2057477511","https://openalex.org/W2058538213","https://openalex.org/W2059885388","https://openalex.org/W2060366601","https://openalex.org/W2063119861","https://openalex.org/W2067076385","https://openalex.org/W2067648136","https://openalex.org/W2069006374","https://openalex.org/W2069750852","https://openalex.org/W2072430635","https://openalex.org/W2074553281","https://openalex.org/W2075093176","https://openalex.org/W2077501220","https://openalex.org/W2078737191","https://openalex.org/W2080992594","https://openalex.org/W2082582661","https://openalex.org/W2089006288","https://openalex.org/W2089745310","https://openalex.org/W2110300847","https://openalex.org/W2114003088","https://openalex.org/W2121292998","https://openalex.org/W2127668566","https://openalex.org/W2132905138","https://openalex.org/W2140151763","https://openalex.org/W2144288821","https://openalex.org/W2148424525","https://openalex.org/W2156012420","https://openalex.org/W2159010139","https://openalex.org/W2167473677","https://openalex.org/W2171047927","https://openalex.org/W2173542734","https://openalex.org/W2315827110","https://openalex.org/W2316392160","https://openalex.org/W2322200946","https://openalex.org/W2325873319","https://openalex.org/W2337762266","https://openalex.org/W2396266812","https://openalex.org/W2409981347","https://openalex.org/W2410310292","https://openalex.org/W2411580022","https://openalex.org/W2533065494","https://openalex.org/W2550999879","https://openalex.org/W2766682498","https://openalex.org/W2793701070","https://openalex.org/W2802251036","https://openalex.org/W2918768857","https://openalex.org/W2923759574","https://openalex.org/W2964344211","https://openalex.org/W2992305306","https://openalex.org/W3081427668","https://openalex.org/W3083637251","https://openalex.org/W3086059121","https://openalex.org/W3104031547","https://openalex.org/W3111232582","https://openalex.org/W3162615688","https://openalex.org/W4213452100","https://openalex.org/W4255420656"],"related_works":["https://openalex.org/W2335570849","https://openalex.org/W2054160223","https://openalex.org/W2105451663","https://openalex.org/W2137956308","https://openalex.org/W4200530443","https://openalex.org/W1976753573","https://openalex.org/W2011916542","https://openalex.org/W1967532320","https://openalex.org/W2583256450","https://openalex.org/W2170876386"],"abstract_inverted_index":{"The":[0],"reliability":[1,284],"of":[2,9,65,134,157],"molecular":[3],"mechanics":[4],"simulations":[5],"to":[6,12,18,29,45,143,186,190,199,253,261],"predict":[7],"effects":[8],"ion":[10],"binding":[11],"proteins":[13],"depends":[14],"on":[15,113],"their":[16],"ability":[17],"simultaneously":[19],"describe":[20,30],"ion-protein,":[21],"ion-water,":[22],"and":[23,32,39,160,167,179,188,214,263,269,289],"protein-water":[24,31],"interactions.":[25],"Force":[26],"fields":[27,147],"(FFs)":[28],"ion-water":[33],"interactions":[34,51,126],"have":[35,40,52],"been":[36,42,54],"constructed":[37],"carefully":[38],"also":[41,53,100],"refined":[43],"routinely":[44],"improve":[46,172,219],"accuracy.":[47],"Descriptions":[48],"for":[49,96,102,267],"ion-protein":[50,125,220],"refined,":[55],"although":[56],"in":[57,69,162,177,234,240,285,291],"an":[58],"<i>a":[59],"posteriori</i>":[60],"manner":[61,237],"through":[62,238],"the":[63,114,120,144,163,276,292],"use":[64],"\"nonbonded-fix":[66],"(NB-fix)\"":[67],"approaches":[68],"which":[70],"parameters":[71],"from":[72,184,201],"default":[73],"Lennard-Jones":[74,254],"mixing":[75],"rules":[76],"are":[77,195,258],"replaced":[78],"with":[79,123,197],"those":[80],"optimized":[81],"against":[82,209],"some":[83],"reference":[84],"data.":[85],"However,":[86],"even":[87],"after":[88],"NB-fix":[89,251],"corrections,":[90],"there":[91],"remains":[92],"a":[93,155,235],"significant":[94],"need":[95],"improvement.":[97],"This":[98],"is":[99],"true":[101],"polarizable":[103,115],"FFs":[104],"that":[105,119,139,169,228,246,275],"include":[106],"self-consistent":[107],"inducible":[108],"moments.":[109],"Our":[110],"recent":[111],"studies":[112],"AMOEBA":[116,164,278],"FF":[117,166,280],"suggested":[118],"problem":[121],"associated":[122],"modeling":[124],"could":[127],"be":[128,232],"alleviated":[129],"by":[130,247],"recalibrating":[131],"polarization":[132],"models":[133],"cation-coordinating":[135],"functional":[136,206],"groups":[137],"so":[138],"they":[140,223],"respond":[141],"better":[142],"high":[145],"electric":[146],"present":[148,153],"near":[149],"ions.":[150,271],"Here,":[151],"we":[152,244,273],"such":[154],"recalibration":[156,217],"carbonyls,":[158],"carboxylates,":[159],"hydroxyls":[161],"protein":[165,279,287],"report":[168],"it":[170],"does":[171,218],"predictions":[173],"substantially\u2500mean":[174],"absolute":[175],"errors":[176,257],"Na<sup>+</sup>-protein":[178],"K<sup>+</sup>-protein":[180],"interaction":[181,221],"energies":[182],"decrease":[183],"8.7":[185],"5.3":[187],"9.6":[189],"6.3":[191],"kcal/mol,":[192,265],"respectively.":[193],"Errors":[194],"computed":[196],"respect":[198],"estimates":[200],"van":[202],"der":[203],"Waals-inclusive":[204],"density":[205],"theory":[207],"benchmarked":[208],"high-level":[210],"quantum":[211],"mechanical":[212],"calculations":[213],"experiments.":[215],"While":[216],"energies,":[222],"still":[224],"remain":[225],"underestimated,":[226],"suggesting":[227],"further":[229,259],"improvements":[230],"can":[231],"made":[233],"systematic":[236],"modifications":[239],"classical":[241],"formalism.":[242],"Nevertheless,":[243],"show":[245,274],"applying":[248],"our":[249],"many-body":[250],"correction":[252],"components,":[255],"these":[256],"reduced":[260],"2.7":[262],"2.6":[264],"respectively,":[266],"Na<sup>+</sup>":[268],"K<sup>+</sup>":[270],"Finally,":[272],"recalibrated":[277],"retains":[281],"its":[282],"intrinsic":[283],"predicting":[286],"structure":[288],"dynamics":[290],"condensed":[293],"phase.":[294]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":6}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2022-10-01T00:00:00"}