> ## Documentation Index > Fetch the complete documentation index at: https://proto.evodesign.org/docs/llms.txt > Use this file to discover all available pages before exploring further. # Structure Alignment > Align and compare 3D protein structures Align and compare three-dimensional protein structures to measure how similar their folds are. Using length-independent similarity scores and superposition, these tools evaluate predicted or designed structures, find structural homologs, and detect distant relationships that sequence comparison alone would miss. * **Input:** two or more 3D structures to compare, or a query structure to search against a set. * **Output:** length-independent similarity scores and an optimal superposition quantifying how alike the folds are.

Steinegger Lab