Structural alignment using the generalized Euclidean distance between conformations
arXiv:0908.0368 · doi:10.1002/qua.22347
Abstract
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 find that using minimal distance as a cost function typically results in an aligned structure that is globally different than that given by an RMSD-based alignment
Accepted in IJQC