Molecular dynamics (MD) simulations with all-atom models, combining adsorption experiments are used to gain a better understanding of affinity interaction between proteins and Cibacron Blue (CB). These interactions with three different proteins are studied. The interactions with CB of different proteins are varying, although HSA and BSA have very similar structures. The influence of pH and salt concentration on these protein-CB bindings is investigated. Different parts of the CB molecule play miscellaneous roles in these interactions. The triazine part plays an important role in the hydrogen bonding between CB and bHb. The binding sites on protein surface differ by changing pH, salt concentration, and protein types. However, two parts seem to be very important to the binding of serum albumins.