Protein folding simulation by all-atom CSAW method

Conditioned self-avoiding walk (CSAW) is a novel ab initio protein folding simulation model based on Langevin equation and Monte-Carlo method. The polypeptide chain is divided into effectively rigid crank units lined by covalent bonds. The only degrees of the freedom are rotations around these bonds. Instead of a hard sphere, the amino acid side chains are modeled by real atom conformation in this paper. The particular feathers of each side chain are considered in calculating the hydrophobic and electrostatic energy in all-atom CSAW. By introducing long range electrostatic interactions, not only the alpha helixes in 1A7W but also beta sheets/strands in 3AIT are successfully simulated for the first time by improved CSAW.