We test molecular level hypotheses for the high thermal stability of α-helical conformations of
alanine-based peptides by performing detailed atomistic simulations of a 20-amino-acid …

A theoretical study to identify the conformational preferences of lysine-based oligopeptides
has been carried out. The solvation free energy and free energy of ionization of the …

In this communication, we have demonstrated that molecular dynamics simulations using a
GB implicit solvation model with the all-atom based force field (CHARMM19) can describe …

This paper contributes to development of a microscopic approach to predicting stable
conformations of proteins in solvent. We report results of the first attempt to combine Monte …

We compare the conformational distributions of Ace‐Ala‐Nme and Ace‐Gly‐Nme sampled
in long simulations with several molecular mechanics (MM) force fields and with a fast …

The hydration free energies of amino acid side chains are an important determinant of
processes that involve partitioning between different environments, including protein folding …

The determination of the folding dynamics of polypeptides and proteins is critical in
characterizing their functions in biological systems. Numerous computational models and …

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

Equilibrium constants for the adsorption of the first water molecule onto a variety of
unsolvated alanine-based peptides have been measured and Δ H° and Δ S° have been …

We present a physically rigorous method to calculate solvent-dependent accessible surface
areas (ASAs) of amino acid residues in unfolded proteins. ASA values will be larger in a …