The relatively simple peptides assembled on the templates are excellent mimic of complex conformational and functional defined binding sites of proteins. The main benefit of experiments with artificial receptors arises from the relative simplicity of the interacting host-guest system allowing the understanding of the rules controlling the model process of the molecular recognition. Efficient modification of molecular receptors by using rational design of their structure or combinatorial methods is crucial for verification of any hypothesis concerning the binding forces or enhancing the binding properties. This approach is presenting promising strategy for understanding mode of action and the control of biological functions of proteins, for designing new pharmaceutically active compounds, new tools for medical diagnostic and molecular sensing.