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cond-mat.soft2001
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…
cond-mat.soft2001
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…
cond-mat.soft2000
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…