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We review simulation and experiments using protein microarrays. Arrays of thousands of proteins with varied functionalities offer parallel, high throughput screening of molecular interactions. Immobilization of probe molecules to a surface or bead allows for location to be equated with identification. The inhomogeneity present because of the material surface can alter the thermodynamic and kinetic recognition properties of the proteins. Understanding the behavior of proteins at interfaces has implications in the design of protein microarrays as well as in the development of other interfacial biomolecular engineering technologies. In this review, we describe current problems when immobilizing peptides/proteins on material surfaces. The interface between experimental and simulation studies is discussed regarding orientation, and conformational stability on materials with varied surface chemistry in terms of protein-surface interactions.