2 citations · 4 across the 7 of their papers we have counts for
4 papers · 1 filter
Sidechain Dynamics and Protein Folding
E. Kussell, J. Shimada, E. I. Shakhnovich
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain…
Excluded Volume in Protein Sidechain Packing
Edo Kussell, Jun Shimada, Eugene I. Shakhnovich
To examine the relationship between sidechain geometry and sidechain packing, we use an all-atom Monte Carlo simulation to sample the large space of sidechain conformations. We stu…
The Folding Thermodynamics and Kinetics of Crambin Using an All-Atom Monte Carlo Simulation
J. Shimada, E. L. Kussell, E. I. Shakhnovich
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relev…
Hiking in the energy landscape in sequence space: a bumpy road to good folders
G. Tiana, R. A. Broglia, E. I. Shakhnovich
With the help of a simple 20 letters, lattice model of heteropolymers, we investigate the energy landscape in the space of designed good-folder sequences. Low-energy sequences form…