SuperPose: a simple server for sophisticated structural superposition

Abstract

The SuperPose web server rapidly and robustly calculates both pairwise and multiple protein structure superpositions using a modified quaternion eigenvalue approach. SuperPose generates sequence alignments, structure alignments, PDB (Protein Data Bank) coordinates and RMSD statistics, as well as difference distance plots and images (both static and interactive) of the superimposed molecules. SuperPose employs a simple interface that requires only PDB files or accession numbers as input. All other superposition decisions are made by the program. SuperPose is uniquely able to superimpose structures that differ substantially in sequence, size or shape. It is also capable of handling a much larger range of superposition queries and situations than many standalone programs and yields results that are intuitively more in agreement with known biological or structural data. The SuperPose web server is freely accessible at http://wishart.biology.ualberta.ca/SuperPose/.

Figure 1

A screenshot montage of SuperPose server output showing the different kinds of graphical and textual output available. Shown are the WebMol viewer, a MolScript image, a pairwise alignment, a difference distance matrix and the RMSD output for a pairwise superposition of 2TRX_A and 3TRX_A (Eschericia coli thioredoxin and human thioredoxin). The two proteins have 29% sequence identity.