With the goal of developing e cient multiple structural alignment methods, we have asked which of the pairwise structure alignment methods lends itself most readily to generalization to multiple structure alignment. A simple linear encoding of the sequence and associated residue conformation can be treated by standard multiple sequence alignment methods.

Multiple sequence alignments are an essential tool for protein structure and function prediction, phylogeny inference and other common tasks in sequence analysis. Recently developed systems have advanced the state of the art with respect to accuracy, ability to scale to thousands of proteins and flexibility in comparing proteins that do not share the same domain architecture. New multiple align...