We seek to understand the link between protein thermodynamics and protein structure in
molecular detail. A classical approach to this problem involves assessing changes in protein …

Despite its theoretical and practical importance, protein folding remains among the most
fundamental unsolved problems in the life sciences. The challenge of predicting folded …

The ff94 force field that is commonly associated with the Amber simulation package is one of
the most widely used parameter sets for biomolecular simulation. After a decade of …

The ensemble folding of two 21-residue α-helical peptides has been studied using all-atom
simulations under several variants of the AMBER potential in explicit solvent using a global …

A 100 ns molecular dynamics simulation of penta‐alanine in explicit water is performed to
study the reversible folding and unfolding of the peptide. Employing a standard principal …

An unfolded state ensemble is generated by using a self-avoiding statistical coil model that
is based on backbone conformational frequencies in a coil library, a subset of the Protein …

Distributions of the backbone dihedral angles of proteins have been studied for over 40
years. While many statistical analyses have been presented, only a handful of probability …

A central issue in protein folding is the degree to which each residue's backbone
conformational preferences stabilize the native state. We have studied the conformational …

Does aqueous solvent discriminate among peptide conformers? To address this question,
we computed the solvation free energy of a blocked, 12‐residue polyalanyl‐peptide in …

There is growing appreciation of the functional relevance of unfolded proteins in biology.
However, unfolded states of proteins have proven inaccessible to the usual techniques for …