Universal similarity measure for comparing protein structures

We introduce a new variant of the root mean square distance (RMSD) for comp aring protein structures iv,hose range of values is independent of protean size. This new, dimensionless measure (relative RMSD, or RRMSD) is zero bet ween identical structures and one between structures that are as globally d issimilar as an average pair of random polypeptides of respective sizes. Th e RRMSD probability distribution between random polypeptides converges to a universal curve as the chain length increases. The correlation coefficient s between aligned random structures are computed as a function of polypepti de size showing taro characteristic lengths of 4.7 and 37 residues. These l engths mark the separation between phases of different structural order bet ween native protein fragments. The implications for threading are discussed . (C) 2001 John Wiley & Sons, Inc.