SuperPose is a freely available web server designed to perform both pairwise and multiple protein structure superpositions. The “Structural superposition” term refers to the rotations and translations performed on one structure to make it match or align with another structure or structures. Structural superposition can be quantified either in terms of similarity or difference measures. The optimal superposition is the one in which the similarity measure is maximized (the former case) or the difference measure (the later case) is minimized. The “SuperPose” web server uses “RMSD” or Root-Mean-Square Deviation as a difference measure to find the optimal pairwise or multiple protein structure superposition. After an initial sequence and secondary structure (in case of low sequence identity) alignment, SuperPose generates a Difference Distance (DD) matrix from the equivalent C-alpha atoms of two molecules. The sequence/structure alignment and DD matrix analysis information is then fed into a modified quaternion eigenvalue algorithm to rapidly perform the structural superposition and calculate the RMSD between aligned regions of two macromolecules.

Superposition may refer to:

• Superposition principle in physics, mathematics, and engineering, describes the overlapping of waves. Particular applications include:
  • Quantum superposition, in quantum physics
  • Superposition theorem, in electronic engineering
• Superposition calculus, used in logic for equational first-order reasoning
• Law of superposition in geology and archaeology, which states that sedimentary layers are deposited in a time sequence, with the oldest on the bottom and the youngest on the top
• In chemistry, a property of two structures that have the same chirality
• Superposition (EP), 2002 album by the band Kling Klang
• Superposition (art installation), an art installation programme commissioned by the Institute of Physics
• In music theory, "reaching over," see Schenkerian analysis#Lines between voices, reaching over