A novel fingerpint for the characterization of protein folds Abstract: A novel fingerprint, in the form of a pair of binary matrices is defined for the characterization of the tertiary structure of proteins that is shown to possess the fold characteristics. It will be shown that it possesses adequate information to find a particular subfold in a protein. Such a fingerprint is useful for comparison on substructures. It also provides a two-dimensional representation of the three-dimensional fold, facilitating the recognition of various patterns. The possibility of using this fingerprint for the detection of common substructures in two different proteins will also be discussed and a heuristic algorithm will be presented that was successful in this task in some cases.