Structural alignment using the generalized Euclidean distance between conformations

The usual Euclidean distance may be generalized to extended objects such as polymers or membranes. Here, this distance is used for the first time as a cost function to align structures. We examined the alignment of extended strands to idealized beta-hairpins of various sizes using several cost functions, including RMSD, MRSD, and the minimal distance. We… (More)