Peptide aptamers are peptides constrained and presented by a scaffold protein 
that are used to study protein function in cells. They are able to disrupt 
protein-protein interactions and to constitute recognition modules that allow 
the creation of a molecular toolkit for the intracellular analysis of protein 
function. The success of peptide aptamer technology is critically dependent on 
the performance of the scaffold. Here, we describe a rational approach to the 
design of a new peptide aptamer scaffold. We outline the qualities that an ideal 
scaffold would need to possess to be broadly useful for in vitro and in vivo 
studies and apply these criteria to the design of a new scaffold, called STM. 
Starting from the small, stable intracellular protease inhibitor stefin A, we 
have engineered a biologically neutral scaffold that retains the stable 
conformation of the parent protein. We show that STM is able to present peptides 
that bind to targets of interest, both in the context of known interactors and 
in library screens. Molecular tools based on our scaffold are likely to be used 
in a wide range of studies of biological pathways, and in the validation of drug 
targets.