Protein Folding Simulations in Kink Model

Abstract: The structure of protein is essentially important for life activities. Proteins can perform their functions only by specific structures. In this thesis, the kink and multi-kink model for protein description are reviewed. It is shown that most of the loop parts in Protein Databank (PDB) can be described by very limited number of kinks within the experimental precision. Furthermore, by applying the model into two well studied real proteins (myoglobin and villin headpiece HP35), it is shown that the multi-kink model gives correct folding pathway and thermal dynamical properties compared with the experimental results for both proteins. In particular, the kink model is computationally inexpensive compared with other existing models. In the last chapter, a new visualization method for the heavy atoms in the side-chain is presented.