2015 Volume 70 Issue 3 Pages 194-199
We have studied folding and dynamics of proteins by using computer simulations. For complex systems such as proteins, simulations tend to get trapped in a few of a huge number of local-minimum energy states. To overcome this multiple minima problem, we have developed generalized-ensemble algorithms. On the other hand, as longer and larger MD regular simulations are performed, it is more important to develop analysis methods to extract the "essential" movements of proteins from simulations. Relaxation mode analysis has been developed to investigate "dynamic" properties of homo-polymer systems. Recently, we have applied the method to protein, hetero-polymer systems. Here, we introduce these methods to investigate protein stability and dynamics using molecular simulations.