Quantitative models and experiments are revealing how the folding free energy surface of a
protein is sculpted by sequence and environment. The sometimes conflicting demands of …

Protein physics is grounded on three fundamental experimental facts: protein, this long
heteropolymer, has a well defined compact three-dimensional structure; this structure can …

Classic techniques for simulating molecular motion, such as the Monte Carlo and molecular
dynamics methods, generate individual motion pathways one at a time and spend most of …

Protein folding mechanisms are probed experimentally using single-point mutant
perturbations. The relative effects on the folding (ϕ-values) and unfolding (1-ϕ) rates are …

In this paper, we present a framework for studying folding problems from a motion-planning
perspective. The version of the motion-planning problem we consider is that of determining …

G-protein-coupled receptors (GPCRs) are ubiquitous integral membrane proteins involved
in diverse cellular signaling processes. Here, we carry out a large-scale ensemble …

The Gō-like models of proteins are constructed based on the knowledge of the native
conformation. However, there are many possible choices of a Hamiltonian for which the …

The misfolding and aggregation of the human prion protein (PrP) is associated with
transmissible spongiform encephalopathies (TSEs). Intermediate conformations forming …

We describe here a general model of the kinetic mechanism of protein folding. In the Foldon
Funnel Model, proteins fold in units of secondary structures, which form sequentially along …

The concept of the protein transition state ensemble (TSE), a collection of the conformations
that have 50% probability to convert rapidly to the folded state and 50% chance to rapidly …