The results of molecular dynamics simulations of different biophysically relevant processes are discussed in the light of experimental investigations. Using detailed electrostatic models for ligands it is shown that agreement with a range of experimental data on structural, energetic and spectroscopic questions can be achieved for Mb interacting with CO. The combination of umbrella sampling and stochastic dynamics allows to follow the rebinding dynamics of CO after photodissociation. The time scales depend on one physically relevant parameter only, the asymptotic separation between the bound and the unbound free energy surface. Proper choice of this parameter gives rebinding times in quanitative agreement with experiment. As a last example the electron coupled proton transfer in Ferredoxin is discussed. Computer simulations suggest that a water molecule can be stabilized around the active site and may be involved in the reaction.