The structural dynamics of biological macromolecules (e.g., proteins) mediate biological function. Computationally, these dynamics are most often studied using molecular dynamics (MD) simulation, which is extremely expensive. In this talk, I will present two practical and accurate alternatives to MD which can be used to study the thermodynamics and kinetics of biomolecular systems, respectively. The first method uses Generalized Belief Propagation to perform free energy calculations. The second method uses Model Checking to formally reason about the kinetics of folding. We will present results relevant to: i) structure prediction and determination, and ii) the rational design of drugs and proteins.