Structural alignment using the generalized Euclidean distance between conformations

Details Structural alignment using the generalized Euclidean distance between conformations Structural alignment using the generalized Euclidean distance between conformations

2009-08-04

arxiv.org/abs/0908.0368v1

Physics

Condensed Matter

Soft Condensed Matter

Accepted in IJQC

Scientific paper

10.1002/qua.22347

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

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