Structural alignment software

This list of structural comparison and alignment software is a compilation of software tools and web portals used in pairwise or multiple structural comparison and structural alignment.

Structural comparison and alignment
Key map:
 * Class:
 * Cα -- Backbone Atom (Cα) Alignment;
 * AllA -- All Atoms Alignment;
 * SSE -- Secondary Structure Elements Alignment;
 * Seq -- Sequence-based alignment
 * Pair -- Pairwise Alignment (2 structures *only*);
 * Multi -- Multiple Structure Alignment (MStA);
 * C-Map -- Contact Map
 * Surf -- Connolly Molecular Surface Alignment
 * SASA -- Solvent Accessible Surface Area
 * Dihed -- Dihedral Backbone Angles
 * PB -- Protein Blocks


 * Flexible:
 * No -- Only rigid-body transformations are considered between the structures being compared.
 * Yes -- The method allows for some flexibility within the structures being compared, such as movements around hinge regions.