Structural alignment is a form of sequence alignment based on comparison of shape.

These alignments attempt to establish equivalences 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..

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