Peptide aptamers are small proteins containing a randomized peptide sequence 
embedded into a stable protein scaffold, such as Thioredoxin. We developed a 
robust method for building a Combinatorial Library of Improved Peptide aptamers 
(CLIPs) of high complexity, containing ≥3×10(10) independent clones, to be used 
as a molecular tool in the study of biological pathways. The Thioredoxin 
scaffold was modified to increase solubility and eliminate aggregation of the 
peptide aptamers. The CLIPs was used in a yeast two-hybrid screen to identify 
peptide aptamers that bind to various domains of the Receptor for Advanced 
Glycation End products (RAGE). NMR spectroscopy was used to identify interaction 
surfaces between the peptide aptamers and RAGE domains. Cellular functional 
assays revealed that in addition to directly interfering with known binding 
sites, peptide aptamer binding distal to ligand sites also inhibits RAGE 
ligand-induced signal transduction. This finding underscores the potential of 
using CLIPs to select allosteric inhibitors of biological targets.