How many protein folding motifs are there?

As the three-dimensional structures of more and more proteins are determined by experiment, discovering substantially novel folding motifs becomes ever rarer. The natural question is how many motifs are there and how many have already been found? In order to answer this in at least one plausible and well-defined sense, we have chosen a quantitative measure of conformational similarity, rho (based on optimal rigid body superposition), and a means of generating all possible three-dimensional chain conformations using the discrete cosine transform. How many different folding motifs there are then depends on the specified cutoff in rho and on the flexibility allowed for the model polypeptide chain. For single chain proteins having no more than about 170 residues and which are not beta-barrels, there are only about 128 motifs that differ by rho > 1.0 (an extremely vague level of similarity), of which so far only 100 have been seen experimentally. The remaining 28 can be viewed as very low-resolution models of either undiscovered novel folds or violations of unknown principles of protein folding.