The binding of proteins to DNA controls many cellular events, including gene expression. In order to work properly, DNA binding proteins need to find their target sequences on DNA with high speed and accuracy. The recognition of the specific DNA binding site requires intimate contacts between the protein and the DNA molecule. However, strong atomic interactions between the two molecules are expected to reduce the velocity of the recognition process. Molecular Dynamics simulations have been used to analyze how protein might move along specif and non-specific DNA sequences, revealing the atomic mechanisms of fast-search and binding site recognition.