The conformational equilibrium of a blocked valine peptide in water and aqueous urea
solution is studied using molecular dynamics simulations. Pair correlation functions indicate …

Quantitative free energy computation involves both using a model that is sufficiently faithful
to the experimental system under study (accuracy) and establishing statistically meaningful …

ABSTRACT A theoretical and computational approach to ab initio structure prediction for
polypeptides in water is described and applied to selected amino acid sequences for testing …

The force fields used in classical modeling studies are semiempirical in nature and rely on
their validation by comparison of simulations with experimental data. The all‐atom replica …

The acidostat method previously developed for performing explicit-solvent molecular
dynamics simulations at constant pH (J. Chem. Phys. 2001, 114, 9706) is applied to …

We investigated the effects of solvents on the intrinsic propensity of peptide backbone
conformations based on molecular dynamics simulations. The results show that compared …

We have studied the potential of mean force of two peptides, one known to adopt a β‐hairpin
and the other an α‐helical conformation in solution. These peptides are, respectively …

An accurate representation of solute–water interactions is necessary for molecular dynamics
simulations of biomolecules that reside in aqueous environments. Modern force fields and …

The interaction of solvent with a polypeptide chain is one of the primary factors controlling
protein folding and stability. In biologically relevant systems, this solvent is most often water …

The central importance of solvent interactions in stabilization of specific protein structure has
long been recognized. Decades ago, Tanford and Kirkwood treated in detail the interaction …