{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T10:28:38Z","timestamp":1787048918338,"version":"build-2736575974"},"reference-count":45,"publisher":"American Chemical Society (ACS)","issue":"8","license":[{"start":{"date-parts":[[2020,7,20]],"date-time":"2020-07-20T00:00:00Z","timestamp":1595203200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2020,7,20]],"date-time":"2020-07-20T00:00:00Z","timestamp":1595203200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2020,7,20]],"date-time":"2020-07-20T00:00:00Z","timestamp":1595203200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100008725","name":"Agencia Nacional de Investigaci??n e Innovaci??n","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002848","name":"Ministerio de Educaci??n, Gobierno de Chile","doi-asserted-by":"publisher","award":["150151"],"award-info":[{"award-number":["150151"]}],"id":[{"id":"10.13039\/501100002848","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002850","name":"Fondo Nacional de Desarrollo Cient??fico y Tecnol??gico","doi-asserted-by":"publisher","award":["1160888"],"award-info":[{"award-number":["1160888"]}],"id":[{"id":"10.13039\/501100002850","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002850","name":"Fondo Nacional de Desarrollo Cient??fico y Tecnol??gico","doi-asserted-by":"publisher","award":["1161014"],"award-info":[{"award-number":["1161014"]}],"id":[{"id":"10.13039\/501100002850","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Structural Convergence Fund for MERCOSUR","award":["COF 03\/11"],"award-info":[{"award-number":["COF 03\/11"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges in achieving an accurate structural and dynamical description of many biological assemblies, particularly to coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or not available for the vast majority of CG force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations using the SIRAH force field. We provide a set of interaction parameters for calcium, magnesium, and zinc ions, which cover more than 80% of the metal-bound structures reported in the PDB. Simulations performed on several proteins and DNA systems show that it is possible to preclude the use of topological constraints by modifying specific Lennard-Jones interactions.<\/jats:p>","DOI":"10.1021\/acs.jcim.0c00160","type":"journal-article","created":{"date-parts":[[2020,7,20]],"date-time":"2020-07-20T12:04:53Z","timestamp":1595246693000},"page":"3935-3943","source":"Crossref","is-referenced-by-count":11,"title":["Coarse-Grained Parameters for Divalent Cations within\nthe SIRAH Force Field"],"prefix":"10.1021","volume":"60","author":[{"given":"Florencia","family":"Klein","sequence":"first","affiliation":[{"name":"Institut Pasteur de Montevideo , Mataojo 2020, ,","place":["Montevideo, Uruguay, 11400"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniela","family":"Ca\u0301ceres","sequence":"additional","affiliation":[{"name":"Universidad de Talca , , 1 Poniente 1141 , ,","place":["Talca, Chile, 3460000"]},{"name":"Universidad de Talca , , Campus Talca, 1 Poniente No. 1141 , ,","place":["Talca, Chile, 3460000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mo\u0301nica A.","family":"Carrasco","sequence":"additional","affiliation":[{"name":"Universidad de Talca , , 1 Poniente 1141 , ,","place":["Talca, Chile, 3460000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan Carlos","family":"Tapia","sequence":"additional","affiliation":[{"name":"Universidad de Talca , , 1 Poniente 1141 , ,","place":["Talca, Chile, 3460000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0182-1444","authenticated-orcid":true,"given":"Julio","family":"Caballero","sequence":"additional","affiliation":[{"name":"Universidad de Talca , , Campus Talca, 1 Poniente No. 1141 , ,","place":["Talca, Chile, 3460000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9624-7849","authenticated-orcid":true,"given":"Jans","family":"Alzate-Morales","sequence":"additional","affiliation":[{"name":"Universidad de Talca , , Campus Talca, 1 Poniente No. 1141 , ,","place":["Talca, Chile, 3460000"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6435-4543","authenticated-orcid":true,"given":"Sergio","family":"Pantano","sequence":"additional","affiliation":[{"name":"Institut Pasteur de Montevideo , Mataojo 2020, ,","place":["Montevideo, Uruguay, 11400"]},{"name":"ShanghaiTech University , , 393 Middle Huaxia Road , ,","place":["Shanghai, China, 201210"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2020,7,20]]},"reference":[{"key":"2026081805083255800_cit1","doi-asserted-by":"publisher","first-page":"10757","DOI":"10.1039\/b907148b","article-title":"Density functional\ntheory for transition metals and\ntransition metal chemistry","volume":"11","author":"Cramer","year":"2009","journal-title":"Phys. Chem. Chem.\nPhys."},{"key":"2026081805083255800_cit2","doi-asserted-by":"publisher","first-page":"5121","DOI":"10.1021\/jp060231d","article-title":"Comparative DFT\nstudy of van der Waals complexes: rare-gas\ndimer, alkaline-earth dimers, zinc dimer, and zinc-rare-gas dimers","volume":"110","author":"Zhao","year":"2006","journal-title":"J. Phys. Chem. A"},{"key":"2026081805083255800_cit3","doi-asserted-by":"publisher","first-page":"4992","DOI":"10.1021\/acs.jctc.5b00524","article-title":"Quantum\neffects in cation interactions with first and second coordination\nshell ligands in metalloproteins","volume":"11","author":"Ngo","year":"2015","journal-title":"J. Chem. Theory\nComput."},{"key":"2026081805083255800_cit4","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1021\/acs.jctc.7b00773","article-title":"Extended\nZinc AMBER Force Field (EZAFF)","volume":"14","author":"Yu","year":"2018","journal-title":"J. Chem. Theory\nComput."},{"key":"2026081805083255800_cit5","doi-asserted-by":"publisher","first-page":"1564","DOI":"10.1021\/acs.chemrev.6b00440","article-title":"Metal Ion Modeling\nUsing Classical Mechanics","volume":"117","author":"Li","year":"2017","journal-title":"Chem. Rev."},{"key":"2026081805083255800_cit6","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1021\/acs.jcim.7b00206","article-title":"A Coarse-Grained Force\nField Parameterized for MgCl2 and\nCaCl2 Aqueous Solutions","volume":"57","author":"Gong","year":"2017","journal-title":"J. Chem.\nInf. 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Chem."},{"key":"2026081805083255800_cit13","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1002\/prot.1138","article-title":"Successful\nmolecular dynamics simulation of two zinc complexes bridged by a hydroxide\nin phosphotriesterase using cationic dummy atom method","volume":"45","author":"Pang","year":"2001","journal-title":"Proteins: Struct., Funct., Genet."},{"key":"2026081805083255800_cit14","doi-asserted-by":"publisher","first-page":"2719","DOI":"10.1021\/acs.jctc.9b00006","article-title":"The SIRAH 2.0 Force Field: Altius,\nFortius, Citius","volume":"15","author":"Machado","year":"2019","journal-title":"J. Chem. Theory Comput."},{"key":"2026081805083255800_cit15","doi-asserted-by":"publisher","first-page":"20180085","DOI":"10.1098\/rsfs.2018.0085","article-title":"From quantum to subcellular\nscales: multi-scale simulation approaches and the SIRAH force field","volume":"9","author":"Machado","year":"2019","journal-title":"Interfaces Focus"},{"key":"2026081805083255800_cit16","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1007\/978-3-319-02624-4_7","article-title":"Assessing\nthe Accuracy of the SIRAH Force Field to\nModel DNA at Coarse Grain Level","volume":"8213","author":"Dans","year":"2013","journal-title":"Lect. Notes\nComput. Sci. Eng."},{"key":"2026081805083255800_cit17","doi-asserted-by":"publisher","first-page":"021903","DOI":"10.1103\/physreve.86.021903","article-title":"Breathing, bubbling,\nand bending: DNA flexibility from multimicrosecond simulations","volume":"86","author":"Zeida","year":"2012","journal-title":"Phys. Rev. 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Basis Dis."},{"key":"2026081805083255800_cit20","doi-asserted-by":"publisher","first-page":"W522","DOI":"10.1093\/nar\/gkm276","article-title":"PDB2PQR:\nExpanding and Upgrading\nAutomated Preparation of Biomolecular Structures for Molecular Simulations","volume":"35","author":"Dolinsky","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2026081805083255800_cit21","doi-asserted-by":"publisher","first-page":"1568","DOI":"10.1093\/bioinformatics\/btw020","article-title":"SIRAH Tools:\nMapping, Backmapping and Visualization\nof Coarse- Grained Models","volume":"32","author":"Machado","year":"2016","journal-title":"Bioinformatics"},{"key":"2026081805083255800_cit22","doi-asserted-by":"publisher","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle Mesh Ewald:\nAn N \u00b7\nlog\u00ad(N) Method for Ewald Sums in Large Systems","volume":"98","author":"Darden","year":"1993","journal-title":"J. Chem. 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Soc."},{"key":"2026081805083255800_cit26","doi-asserted-by":"publisher","first-page":"471","DOI":"10.1016\/j.bbrc.2016.03.034","article-title":"Solution Structure\nof the 13th C2H2 Zinc Finger of Miz-1","volume":"473","author":"Tremblay","year":"2016","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2026081805083255800_cit27","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1016\/j.abb.2010.08.014","article-title":"Structures of mouse\nSOD1 and human\/mouse SOD1 chimeras","volume":"503","author":"Seetharaman","year":"2010","journal-title":"Arch. Biochem.\nBiophys."},{"key":"2026081805083255800_cit28","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3000141","article-title":"Molecular\nrecognition and maturation of SOD1 by its evolutionarily destabilized\ncognate chaperone hCCS","volume":"17","author":"Sala","year":"2019","journal-title":"PLoS Biol."},{"key":"2026081805083255800_cit29","doi-asserted-by":"publisher","first-page":"1171","DOI":"10.1016\/s0969-2126(96)00125-6","article-title":"Zif268 protein-DNA\ncomplex refined at 1.6 \u00c5: a model system for understanding zinc\nfinger-DNA interactions","volume":"4","author":"Elrod-Erickson","year":"1996","journal-title":"Structure"},{"key":"2026081805083255800_cit30","doi-asserted-by":"publisher","first-page":"809","DOI":"10.1126\/science.2028256","article-title":"Zinc finger-DNA recognition:\ncrystal structure of a Zif268-DNA complex\nat 2.1 A","volume":"252","author":"Pavletich","year":"1991","journal-title":"Sciene"},{"key":"2026081805083255800_cit31","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1016\/j.jmb.2004.12.046","article-title":"Crystal\nStructure of AhpE from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin","volume":"346","author":"Li","year":"2005","journal-title":"J. Mol. Biol."},{"key":"2026081805083255800_cit32","first-page":"23","article-title":"Calcium: A Matter\nof Life or Death","volume-title":"The Evolution of the Biochemistry\nof Calcium","author":"Williams","year":"2007"},{"key":"2026081805083255800_cit33","doi-asserted-by":"publisher","first-page":"15879","DOI":"10.1074\/jbc.273.26.15879","article-title":"C2-domains, Structure and Function of a\nUniversal Ca2+-binding Domain","volume":"273","author":"Rizo","year":"1998","journal-title":"J.\nBiol. Chem."},{"key":"2026081805083255800_cit34","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1016\/j.ijbiomac.2016.10.083","article-title":"Int. Structural analysis\nof Ca2+ -binding pocket of synaptotagmin 5 C2A domain","volume":"95","author":"Qiu","year":"2017","journal-title":"J. Biol. Macromol."},{"key":"2026081805083255800_cit35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.2005653","article-title":"Structural\nbasis for overhang excision\nand terminal unwinding of DNA duplexes by TREX1","volume":"16","author":"Huang","year":"2018","journal-title":"PLoS Biol."},{"key":"2026081805083255800_cit36","doi-asserted-by":"publisher","first-page":"5141","DOI":"10.1021\/jp909132a","article-title":"Solvation\nof Magnesium Dication: Molecular Dynamics Simulation and Vibrational\nSpectroscopic Study of Magnesium Chloride in Aqueous Solutions","volume":"114","author":"Callahan","year":"2010","journal-title":"J. Phys. Chem. A"},{"key":"2026081805083255800_cit37","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.1021\/ja308952y","article-title":"Small-molecule\nbinding to the DNA\nminor groove is mediated by a conserved water cluster","volume":"135","author":"Wei","year":"2013","journal-title":"J. Am. Chem. Soc."},{"key":"2026081805083255800_cit38","unstructured":"Klein, F.; Barrera, E.; Garay, P.; Machado, M.; Son\u0303ora, M.; Pantano, S.\n          SIRAH-CoV2 Initiative: Papain-like\nProtease (PDB id: 6W9C) (DOI: 10.5281\/zenodo.3766270)."},{"key":"2026081805083255800_cit39","unstructured":"Klein, F.; Barrera, E.; Garay, P.; Machado, M.; Son\u0303ora, M.; Pantano, S.\n          SIRAH-CoV2 Initiative:\nRNA Binding\nDomain of Nucleocapsid Phosphoprotein (PDB id: 6VYO) (DOI: 10.5281\/zenodo.3747621)."},{"key":"2026081805083255800_cit40","unstructured":"Son\u0303ora, M.; Barrera, E.; Garay, P.; Klein, F.; Machado, M.; Son\u0303ora, M.; Pantano, S.\n          SIRAH-CoV2 Initiative: NSP16-NSP10\nComplex (PDB id: 6W4H) (DOI: 10.5281\/zenodo.3779057)."},{"key":"2026081805083255800_cit41","unstructured":"Son\u0303ora, M.; Barrera, E.; Garay, P.; Klein, F.; Machado, M.; Son\u0303ora, M.; Pantano, S.\n          SIRAH-CoV2\nInitiative: RNA-dependent\nRNA Polymerase in Complex with Cofactors Nsp7 and Nsp8 (PDB id: 7BTF) (DOI: 10.5281\/zenodo.3865479)."},{"key":"2026081805083255800_cit42","doi-asserted-by":"publisher","first-page":"3437","DOI":"10.1021\/acs.jcim.9b00235","article-title":"New Zinc Ion Parameters Suitable\nfor Classical MD Simulations of Zinc Metallopeptidases","volume":"59","author":"Tomic\u0301","year":"2019","journal-title":"J. Chem. Inf. Model."},{"key":"2026081805083255800_cit43","doi-asserted-by":"publisher","first-page":"2643","DOI":"10.1021\/acs.jpca.6b12969","article-title":"Interaction Energies in Complexes\nof Zn and Amino-Acids: a Comparison of Ab-Initio and Force Field based\nCalculations","volume":"121","author":"Ahlstrand","year":"2017","journal-title":"J. Phys. Chem. A"},{"key":"2026081805083255800_cit44","doi-asserted-by":"publisher","first-page":"8432","DOI":"10.1039\/c7cp08185e","article-title":"New tricks for old dogs: improving the accuracy of\nbiomolecular force fields by pair-specific corrections to non-bonded\ninteractions","volume":"20","author":"Yoo","year":"2018","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2026081805083255800_cit45","article-title":"Parameterization\nof Divalent Cations for Coarse-Grained Simulations","author":"Klein","year":"2020","journal-title":"ChemRxiv"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.0c00160","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/60\/8\/3935\/9374764\/ci0c00160.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/60\/8\/3935\/9374764\/ci0c00160.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T09:59:24Z","timestamp":1787047164000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article\/60\/8\/3935\/874251\/Coarse-Grained-Parameters-for-Divalent-Cations"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,7,20]]},"references-count":45,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2020,7,20]]},"published-print":{"date-parts":[[2020,8,24]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.0c00160","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv.11881716.v1","asserted-by":"object"}]},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,7,20]]}}}