Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

Implicit solvent models for biomolecular simulations are reviewed and their underlying
statistical mechanical basis is discussed. The fundamental quantity that implicit models seek …

The use of molecular dynamics simulation to investigate the properties of hydration water
around proteins is outlined. A variety of structural and dynamical properties of the protein …

We present a CPU efficient protocol for refinement of protein structures in a thin layer of
explicit solvent and energy parameters with completely revised dihedral angle terms. Our …

Starting from the eight B3LYP/6-31G* optimized N-acetyl-l-alanine N '-methylamide (AAMA)
structures recently reported by Jalkanen and Suhai, we studied the effect of hydration on the …

Abbreviations: ArgRNz Arg Repressor N-terminal domain; dsRBD: double-stranded RNA
binding domain; PH: Pleckstrin homology; KH: K homology; PDI: Protein disulphide …

Pressure is a thermodynamic variable which is particularly suitable for exploration of the
properties of biological macromolecules. For proteins, in particular, denaturation induced by …

The use of parallel tempering or replica exchange molecular dynamics (REMD) simulations
has facilitated the exploration of free energy landscapes for complex molecular systems, but …

We present a new hybrid explicit/implicit solvent method for dynamics simulations of
macromolecular systems. The method models explicitly the hydration of the solute by either …

The calculation of protein interaction energetics is of fundamental interest, yet accurate
quantities are difficult to obtain due to the complex and dynamic nature of protein interfaces …