143 related articles for article (PubMed ID: 34241062)
1. Extended magnesium and calcium force field parameters for accurate ion-nucleic acid interactions in biomolecular simulations.
Cruz-León S; Grotz KK; Schwierz N
J Chem Phys; 2021 May; 154(17):171102. PubMed ID: 34241062
[TBL] [Abstract][Full Text] [Related]
2. Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties.
Grotz KK; Cruz-León S; Schwierz N
J Chem Theory Comput; 2021 Apr; 17(4):2530-2540. PubMed ID: 33720710
[TBL] [Abstract][Full Text] [Related]
3. Force fields for divalent cations based on single-ion and ion-pair properties.
Mamatkulov S; Fyta M; Netz RR
J Chem Phys; 2013 Jan; 138(2):024505. PubMed ID: 23320702
[TBL] [Abstract][Full Text] [Related]
4. Force fields for monovalent and divalent metal cations in TIP3P water based on thermodynamic and kinetic properties.
Mamatkulov S; Schwierz N
J Chem Phys; 2018 Feb; 148(7):074504. PubMed ID: 29471634
[TBL] [Abstract][Full Text] [Related]
5. Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations.
Allnér O; Nilsson L; Villa A
J Chem Theory Comput; 2012 Apr; 8(4):1493-502. PubMed ID: 26596759
[TBL] [Abstract][Full Text] [Related]
6. Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids.
Panteva MT; Giambaşu GM; York DM
J Phys Chem B; 2015 Dec; 119(50):15460-70. PubMed ID: 26583536
[TBL] [Abstract][Full Text] [Related]
7. Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D.
Grotz KK; Schwierz N
J Chem Theory Comput; 2022 Jan; 18(1):526-537. PubMed ID: 34881568
[TBL] [Abstract][Full Text] [Related]
8. Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations.
Panteva MT; Giambaşu GM; York DM
J Comput Chem; 2015 May; 36(13):970-82. PubMed ID: 25736394
[TBL] [Abstract][Full Text] [Related]
9. Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.
Yoo J; Wilson J; Aksimentiev A
Biopolymers; 2016 Oct; 105(10):752-63. PubMed ID: 27144470
[TBL] [Abstract][Full Text] [Related]
10. Calcium inhibition of ribonuclease H1 two-metal ion catalysis.
Rosta E; Yang W; Hummer G
J Am Chem Soc; 2014 Feb; 136(8):3137-44. PubMed ID: 24499076
[TBL] [Abstract][Full Text] [Related]
11. Interaction of charged amino-acid side chains with ions: an optimization strategy for classical force fields.
Kahlen J; Salimi L; Sulpizi M; Peter C; Donadio D
J Phys Chem B; 2014 Apr; 118(14):3960-72. PubMed ID: 24649981
[TBL] [Abstract][Full Text] [Related]
12. Magnesium force fields for OPC water with accurate solvation, ion-binding, and water-exchange properties: Successful transfer from SPC/E.
Grotz KK; Schwierz N
J Chem Phys; 2022 Mar; 156(11):114501. PubMed ID: 35317575
[TBL] [Abstract][Full Text] [Related]
13. Assessing the Current State of Amber Force Field Modifications for DNA.
Galindo-Murillo R; Robertson JC; Zgarbová M; Šponer J; Otyepka M; Jurečka P; Cheatham TE
J Chem Theory Comput; 2016 Aug; 12(8):4114-27. PubMed ID: 27300587
[TBL] [Abstract][Full Text] [Related]
14. A magnesium-induced triplex pre-organizes the SAM-II riboswitch.
Roy S; Lammert H; Hayes RL; Chen B; LeBlanc R; Dayie TK; Onuchic JN; Sanbonmatsu KY
PLoS Comput Biol; 2017 Mar; 13(3):e1005406. PubMed ID: 28248966
[TBL] [Abstract][Full Text] [Related]
15. Rational design of ion force fields based on thermodynamic solvation properties.
Horinek D; Mamatkulov SI; Netz RR
J Chem Phys; 2009 Mar; 130(12):124507. PubMed ID: 19334851
[TBL] [Abstract][Full Text] [Related]
16. Coarse-Grained Parameters for Divalent Cations within the SIRAH Force Field.
Klein F; Cáceres D; Carrasco MA; Tapia JC; Caballero J; Alzate-Morales J; Pantano S
J Chem Inf Model; 2020 Aug; 60(8):3935-3943. PubMed ID: 32687361
[TBL] [Abstract][Full Text] [Related]
17. Understanding nucleic acid-ion interactions.
Lipfert J; Doniach S; Das R; Herschlag D
Annu Rev Biochem; 2014; 83():813-41. PubMed ID: 24606136
[TBL] [Abstract][Full Text] [Related]
18. Recalibrating the calcium trap in amino acid carboxyl groups
Koskamp JA; Ruiz Hernandez SE; de Leeuw NH; Wolthers M
Phys Chem Chem Phys; 2023 Jan; 25(2):1220-1235. PubMed ID: 36524712
[TBL] [Abstract][Full Text] [Related]
19. Modeling Electronic Polarizability Changes in the Course of a Magnesium Ion Water Ligand Exchange Process.
Kurnikov IV; Kurnikova M
J Phys Chem B; 2015 Aug; 119(32):10275-86. PubMed ID: 26109375
[TBL] [Abstract][Full Text] [Related]
20. Solvation structures of calcium and magnesium ions in water with the presence of hydroxide: a study by deep potential molecular dynamics.
Liu J; Liu R; Cao Y; Chen M
Phys Chem Chem Phys; 2023 Jan; 25(2):983-993. PubMed ID: 36519362
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]