… Ion condensation around such molecules can be predicted … distribution of ions around
hydration shells of nucleic acids. … or occupancy of the hydration water molecule at this site. The …

… ion-binding including the de novo prediction of inner-sphere … AMBER force fields for nucleic
acids and proteins have been … Hereby, we follow each water molecule individually through …

… first solvation shell are key to predicting how … water molecules were described by the TIP3P
water model. DNA was modeled by the AMBER99SB force field with ParmBSC0 nucleic acid …

… and the binding affinity to nucleic acids in TIP3P water. Since … Mg 2+ , or to predict ion binding
sites in biomolecular simulations… one water molecule in the first hydration shell with a water …

… predict that all explicit water molecules are bound to the ion … additional water molecules in
the second solvation shell of the ion… using the optimized geometries and the DFT methods and …

… binding (as opposed to site binding) and are unresolved even in … this theory does not predict
the dependence of ΔN on ionic … Solvation of ions and macromolecules is neglected and ions …

… ] allowing waters and cations site-prediction during … nucleic acids is the electrostatic
distribution of the charges, which is associated with the solvation effect of water molecules and ions …

… water placement and is the only well-validated method to-date, for water placement for nucleic
acids… -date for predicting tightly-bound water molecules in nucleic acid-ligand complexes. …

… optimal positions of water molecules for protein hydration, ii) … of the techniques used for the
prediction of water molecules’ … large cavities and protein-nucleic acids complexes, that are …

… distribution of ions around nucleic acids. Atomic details of the … system, ion type, used water
model, and size of solvate box … inclination predicted by the OL3 force field (OPC water model) …