Structural alignment attempts to establish homology between two or more
polymer structures based on their shape and three-dimensional
conformation. This process is usually applied to
protein tertiary structures but can also be used for large
RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no
a priori knowledge of equivalent positions. Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard
sequence alignment techniques. Structural alignment can therefore be used to imply
evolutionary relationships between proteins that share very little common sequence. However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of
convergent evolution by which multiple unrelated
amino acid sequences converge on a common
tertiary structure.