Synthetic agents that disrupt intracellular protein–protein interactions (PPIs) are desirable for elucidating cellular signaling networks and for development of new therapeutics. However, designing large cell-permeable molecules that are equipped with many functional groups necessary for binding to protein interfaces still remains a challenge. Recent studies of self-assembling small molecules have shed light on the robustness of approaches based on artificial synthetic platforms towards protein surface recognition with a wide range of applications, including library synthesis, protein sensing, and in situ generation of bioactive molecules. This review illustrates recently developed strategies of protein-templated assembly, in which self-assembly of small molecules is induced by binding to a targeted protein. Following chemical reactions between the fragments results in generation of a conjugated molecule, which is capable of modulating functions of water-exposed protein surfaces.