The alanine dipeptide1 (see Figure 1) has served as a paradigm for theoretical studies of
backbone conformationalequilibria in proteins. This is because the dipeptide contains many …

In this paper we discuss the problem of including solvation free energies in evaluating the
relative stabilities of loops in proteins. A conformational search based on a gas‐phase …

It has long been proposed that much of the information encoding how a protein folds is
contained locally in the peptide chain. Here we present a large-scale simulation study …

We have used molecular dynamics simulations to determine the stability in water of a model
β-sheet formed by two alanine dipeptide molecules with two intermolecular hydrogen bonds …

Amino acids in peptides and proteins display distinct preferences for α-helical, β-strand, and
other conformational states. Various physicochemical reasons for these preferences have …

We compare simulations using the generalized Born/surface area (GB/SA) implicit solvent
model with simulations using explicit solvent (transferable intermolecular potential 3 point …

The structures and properties of unsolvated peptides large enough to possess secondary
structure have been examined by experiments and simulations. Some of the factors that …

The partitioning of amino acids between water and apolar environments is of vital
importance in protein function and drug delivery. Here we present an extensive benchmark …

Amino acid residues of unfolded peptides in water sample only a few basins in the
Ramachandran plot, including prominent polyproline II-like (pPII) conformations. Dynamics …

Here, we compare the distributions of main chain (Φ, Ψ) angles (ie, Ramachandran maps) of
the 20 naturally occurring amino acids in three contexts:(i) molecular dynamics (MD) …