Multi-scale properties of biological protein materials have been the focal point of extensive investigations over the past decades, leading to formation of a research field that connects biology and materials science, referred to as materiomics. In this chapter we review atomistic based modeling approaches applied to study the scale-dependent mechanical behavior of biological protein materials, focused on mechanical deformation and failure properties. Specific examples are provided to illustrate the application of numerical methods that link atomistic to mesoscopic and larger continuum scales. The discussion includes the formulation of atomistic simulation methods, as well as examples that demonstrate their application in case studies focused on size effects of the fracture behavior of protein materials. The link of atomistic scale features of molecular structures to structural scales at length-scales of micrometers will be discussed in the analysis of the mechanics of a simple model of the nuclear lamin network, revealing how protein networks with structural flaws cope with mechanical load.