{"id":"https://openalex.org/W2966088763","doi":"https://doi.org/10.1021/acs.jcim.9b00407","title":"Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands","display_name":"Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands","publication_year":2019,"publication_date":"2019-08-06","ids":{"openalex":"https://openalex.org/W2966088763","doi":"https://doi.org/10.1021/acs.jcim.9b00407","mag":"2966088763","pmid":"https://pubmed.ncbi.nlm.nih.gov/31385702"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00407","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00407","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047298129","display_name":"Marina Macchiagodena","orcid":"https://orcid.org/0000-0002-3151-718X"},"institutions":[{"id":"https://openalex.org/I45084792","display_name":"University of Florence","ror":"https://ror.org/04jr1s763","country_code":"IT","type":"education","lineage":["https://openalex.org/I45084792"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marina Macchiagodena","raw_affiliation_strings":["Dipartimento di Chimica \u201cUgo Schiff\u201d, Universit\u00e0 degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy"],"raw_orcid":"https://orcid.org/0000-0002-3151-718X","affiliations":[{"raw_affiliation_string":"Dipartimento di Chimica \u201cUgo Schiff\u201d, Universit\u00e0 degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I45084792"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022056360","display_name":"Marco Pagliai","orcid":"https://orcid.org/0000-0003-0240-161X"},"institutions":[{"id":"https://openalex.org/I45084792","display_name":"University of Florence","ror":"https://ror.org/04jr1s763","country_code":"IT","type":"education","lineage":["https://openalex.org/I45084792"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Marco Pagliai","raw_affiliation_strings":["Dipartimento di Chimica \u201cUgo Schiff\u201d, Universit\u00e0 degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy"],"raw_orcid":"https://orcid.org/0000-0003-0240-161X","affiliations":[{"raw_affiliation_string":"Dipartimento di Chimica \u201cUgo Schiff\u201d, Universit\u00e0 degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I45084792"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079457434","display_name":"Claudia Andreini","orcid":"https://orcid.org/0000-0003-4329-8225"},"institutions":[{"id":"https://openalex.org/I4210144939","display_name":"Interuniversity Consortium for Magnetic Resonance","ror":"https://ror.org/04v403p80","country_code":"IT","type":"education","lineage":["https://openalex.org/I4210144939"]},{"id":"https://openalex.org/I45084792","display_name":"University of Florence","ror":"https://ror.org/04jr1s763","country_code":"IT","type":"education","lineage":["https://openalex.org/I45084792"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Claudia Andreini","raw_affiliation_strings":["Dipartimento di Chimica \u201cUgo Schiff\u201d, Universit\u00e0 degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","Magnetic Resonance Center (CERM)-Universit\u00e0 degli Studi di Firenze, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Chimica \u201cUgo Schiff\u201d, Universit\u00e0 degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I45084792"]},{"raw_affiliation_string":"Magnetic Resonance Center (CERM)-Universit\u00e0 degli Studi di Firenze, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084306542","display_name":"Antonio Rosato","orcid":"https://orcid.org/0000-0001-6172-0368"},"institutions":[{"id":"https://openalex.org/I4210144939","display_name":"Interuniversity Consortium for Magnetic Resonance","ror":"https://ror.org/04v403p80","country_code":"IT","type":"education","lineage":["https://openalex.org/I4210144939"]},{"id":"https://openalex.org/I45084792","display_name":"University of Florence","ror":"https://ror.org/04jr1s763","country_code":"IT","type":"education","lineage":["https://openalex.org/I45084792"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Antonio Rosato","raw_affiliation_strings":["Dipartimento di Chimica \u201cUgo Schiff\u201d, Universit\u00e0 degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","Magnetic Resonance Center (CERM)-Universit\u00e0 degli Studi di Firenze, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy"],"raw_orcid":"https://orcid.org/0000-0001-6172-0368","affiliations":[{"raw_affiliation_string":"Dipartimento di Chimica \u201cUgo Schiff\u201d, Universit\u00e0 degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I45084792"]},{"raw_affiliation_string":"Magnetic Resonance Center (CERM)-Universit\u00e0 degli Studi di Firenze, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I4210144939","https://openalex.org/I45084792"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072028484","display_name":"Piero Procacci","orcid":"https://orcid.org/0000-0003-2667-3847"},"institutions":[{"id":"https://openalex.org/I45084792","display_name":"University of Florence","ror":"https://ror.org/04jr1s763","country_code":"IT","type":"education","lineage":["https://openalex.org/I45084792"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Piero Procacci","raw_affiliation_strings":["Dipartimento di Chimica \u201cUgo Schiff\u201d, Universit\u00e0 degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy"],"raw_orcid":"https://orcid.org/0000-0003-2667-3847","affiliations":[{"raw_affiliation_string":"Dipartimento di Chimica \u201cUgo Schiff\u201d, Universit\u00e0 degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy","institution_ids":["https://openalex.org/I45084792"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5022056360"],"corresponding_institution_ids":["https://openalex.org/I45084792"],"apc_list":null,"apc_paid":null,"fwci":2.65,"has_fulltext":false,"cited_by_count":68,"citation_normalized_percentile":{"value":0.90904708,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"59","issue":"9","first_page":"3803","last_page":"3816"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9997000098228455,"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":0.9997000098228455,"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/T11162","display_name":"Enzyme Structure and Function","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":0.9984999895095825,"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/histidine","display_name":"Histidine","score":0.8194085359573364},{"id":"https://openalex.org/keywords/cysteine","display_name":"Cysteine","score":0.7298592925071716},{"id":"https://openalex.org/keywords/zinc","display_name":"Zinc","score":0.6941336393356323},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5756233930587769},{"id":"https://openalex.org/keywords/zinc-finger","display_name":"Zinc finger","score":0.5047575235366821},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3596445918083191},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.19508129358291626},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.14698079228401184}],"concepts":[{"id":"https://openalex.org/C2778460671","wikidata":"https://www.wikidata.org/wiki/Q485277","display_name":"Histidine","level":3,"score":0.8194085359573364},{"id":"https://openalex.org/C2779201268","wikidata":"https://www.wikidata.org/wiki/Q186474","display_name":"Cysteine","level":3,"score":0.7298592925071716},{"id":"https://openalex.org/C535196362","wikidata":"https://www.wikidata.org/wiki/Q758","display_name":"Zinc","level":2,"score":0.6941336393356323},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5756233930587769},{"id":"https://openalex.org/C24284526","wikidata":"https://www.wikidata.org/wiki/Q204785","display_name":"Zinc finger","level":4,"score":0.5047575235366821},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3596445918083191},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.19508129358291626},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.14698079228401184},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003545","descriptor_name":"Cysteine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006639","descriptor_name":"Histidine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006639","descriptor_name":"Histidine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006639","descriptor_name":"Histidine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","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":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000378","qualifier_name":"metabolism","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},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.9b00407","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00407","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:31385702","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31385702","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:flore.unifi.it:2158/1172777","is_oa":false,"landing_page_url":"http://hdl.handle.net/2158/1172777","pdf_url":null,"source":{"id":"https://openalex.org/S4306402033","display_name":"Florence Research (University of Florence)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45084792","host_organization_name":"University of Florence","host_organization_lineage":["https://openalex.org/I45084792"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.7599999904632568,"display_name":"Affordable and clean energy"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320322648","display_name":"Universit\u00e0 degli Studi di Firenze","ror":"https://ror.org/04jr1s763"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":98,"referenced_works":["https://openalex.org/W615683476","https://openalex.org/W1625910593","https://openalex.org/W1810694562","https://openalex.org/W1965830367","https://openalex.org/W1965879055","https://openalex.org/W1966479051","https://openalex.org/W1967751997","https://openalex.org/W1970410138","https://openalex.org/W1970559654","https://openalex.org/W1976161355","https://openalex.org/W1979100273","https://openalex.org/W1979401635","https://openalex.org/W1980107025","https://openalex.org/W1981368803","https://openalex.org/W1982130835","https://openalex.org/W1982869342","https://openalex.org/W1982952953","https://openalex.org/W1984104023","https://openalex.org/W1984155407","https://openalex.org/W1984552405","https://openalex.org/W1989060947","https://openalex.org/W1991380481","https://openalex.org/W1991458732","https://openalex.org/W1995981464","https://openalex.org/W1998524463","https://openalex.org/W1998556716","https://openalex.org/W2000770615","https://openalex.org/W2010076108","https://openalex.org/W2014166972","https://openalex.org/W2017829285","https://openalex.org/W2019321155","https://openalex.org/W2023271753","https://openalex.org/W2034584345","https://openalex.org/W2035266068","https://openalex.org/W2035515922","https://openalex.org/W2035594105","https://openalex.org/W2037813023","https://openalex.org/W2040521312","https://openalex.org/W2041149343","https://openalex.org/W2049475242","https://openalex.org/W2049623642","https://openalex.org/W2050470003","https://openalex.org/W2053762647","https://openalex.org/W2053999299","https://openalex.org/W2055337326","https://openalex.org/W2057477511","https://openalex.org/W2064499871","https://openalex.org/W2066662117","https://openalex.org/W2067174909","https://openalex.org/W2070753604","https://openalex.org/W2073714240","https://openalex.org/W2074386125","https://openalex.org/W2077212468","https://openalex.org/W2082439356","https://openalex.org/W2082817887","https://openalex.org/W2085247476","https://openalex.org/W2086957099","https://openalex.org/W2091662140","https://openalex.org/W2105796999","https://openalex.org/W2105807617","https://openalex.org/W2108313514","https://openalex.org/W2110800533","https://openalex.org/W2112310296","https://openalex.org/W2125273086","https://openalex.org/W2127378318","https://openalex.org/W2128063462","https://openalex.org/W2128572087","https://openalex.org/W2140151763","https://openalex.org/W2145054879","https://openalex.org/W2145098687","https://openalex.org/W2149801992","https://openalex.org/W2150583375","https://openalex.org/W2156809591","https://openalex.org/W2160194356","https://openalex.org/W2160544821","https://openalex.org/W2161605421","https://openalex.org/W2164122903","https://openalex.org/W2166865790","https://openalex.org/W2171268876","https://openalex.org/W2230728100","https://openalex.org/W2269059522","https://openalex.org/W2312730204","https://openalex.org/W2404280981","https://openalex.org/W2520301867","https://openalex.org/W2559472967","https://openalex.org/W2562478482","https://openalex.org/W2589236205","https://openalex.org/W2604733798","https://openalex.org/W2767229396","https://openalex.org/W2770852490","https://openalex.org/W2801031128","https://openalex.org/W2892247945","https://openalex.org/W2898210859","https://openalex.org/W2898478523","https://openalex.org/W2901261450","https://openalex.org/W4231059664","https://openalex.org/W4255499680","https://openalex.org/W4388245583"],"related_works":["https://openalex.org/W2067936761","https://openalex.org/W2417131764","https://openalex.org/W2070652985","https://openalex.org/W2049444949","https://openalex.org/W4233265360","https://openalex.org/W2085980434","https://openalex.org/W1969212998","https://openalex.org/W2081911437","https://openalex.org/W1260787347","https://openalex.org/W2051885497"],"abstract_inverted_index":{"We":[0],"developed":[1],"and":[2,33,63,115,118,206],"validated":[3],"a":[4,90,109],"novel":[5],"force":[6,23],"field":[7,24],"in":[8,128,147],"the":[9,12,16,30,34,48,52,56,60,98,129,148,159,162,177,183,187,200,204,209],"context":[10],"of":[11,18,41,51,59,66,69,93,102,122,161,208],"AMBER":[13],"parameterization":[14,211],"for":[15,47,155,212],"simulation":[17],"zinc(II)-binding":[19,143,184,213],"proteins.":[20,214],"The":[21,77,105,193],"proposed":[22,210],"assumes":[25],"nonbonded":[26],"spherical":[27],"interactions":[28],"between":[29],"central":[31],"zinc(II)":[32,103,110,126,156],"coordinating":[35,61],"residues.":[36],"A":[37],"crucial":[38],"innovative":[39],"aspect":[40],"our":[42,153],"approach":[43],"is":[44],"to":[45,72,173],"account":[46],"polarization":[49],"effects":[50],"cation":[53],"by":[54,83,113,181],"redefining":[55],"atomic":[57],"charges":[58],"residues":[62,117],"an":[64],"adjustment":[65],"Lennard-Jones":[67],"parameters":[68],"Zn-interacting":[70],"atoms":[71],"reproduce":[73],"mean":[74,170],"distance":[75],"distributions.":[76],"optimal":[78],"transferable":[79],"parametrization":[80],"was":[81,179],"obtained":[82],"performing":[84],"accurate":[85],"quantum":[86],"mechanical":[87],"calculations":[88],"on":[89,141],"training":[91,149],"set":[92],"high-quality":[94],"protein":[95],"structures,":[96],"encompassing":[97],"most":[99],"common":[100],"folds":[101],"sites.":[104],"addressed":[106],"sites":[107,127,157],"contain":[108],"ion":[111],"tetra-coordinated":[112],"histidine":[114],"cysteine":[116],"represent":[119],"about":[120],"70%":[121],"all":[123],"physiologically":[124],"relevant":[125],"Protein":[130],"Data":[131],"Bank.":[132],"Molecular":[133],"dynamics":[134],"simulations":[135],"with":[136,165,199],"explicit":[137],"solvent,":[138],"carried":[139],"out":[140],"several":[142],"proteins":[144],"not":[145],"included":[146],"set,":[150],"show":[151],"that":[152],"model":[154,178],"preserves":[158],"tetra-coordination":[160],"metal":[163],"site":[164],"remarkable":[166],"stability,":[167],"yielding":[168],"zinc(II)-X":[169],"distances":[171],"similar":[172],"experimental":[174,201],"data.":[175],"Finally,":[176],"tested":[180],"evaluating":[182],"affinities,":[185],"using":[186],"alchemical":[188],"free":[189],"energy":[190],"perturbation":[191],"approach.":[192],"calculated":[194],"dissociation":[195],"constants":[196],"correlate":[197],"satisfactorily":[198],"counterpart":[202],"demonstrating":[203],"validity":[205],"transferability":[207]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":5}],"updated_date":"2026-06-08T08:47:23.578185","created_date":"2025-10-10T00:00:00"}
