Molecular recognition and mechanical properties of proteins govern molecular processes in the cell that can cause disease and can be targeted for drug design. Single molecule measurement techniques have greatly advanced knowledge but cannot resolve enough detail to be interpreted in terms of protein structure. We seek to complement the observations through so-called Steered Molecular Dynamics (SMD) simulations that link directly to experiments and provide atomic-level descriptions of the underlying events. Such a research program has been initiated in our group and has involved, for example, studies of elastic properties of immunoglobulin and fibronectin domains as well as the binding of biotin and avidin. In this article we explain the SMD method and suggest how it can be applied to the function of three systems that are the focus of modern molecular biology research: force transduction by the muscle protein titin and extracellular matrix protein fibronectin, recognition of antibody-antigene pairs, and ion selective conductivity of the K+ channel.