SuperPose

SuperPose performs rapid and robust protein structure superpositions using a modified quaternion eigenvalue approach to produce pairwise and multiple alignments for comparative structural analysis.

Key Features:

• Modified quaternion eigenvalue approach: Applies a modified quaternion eigenvalue algorithm to compute accurate superpositions.
• Pairwise and multiple structure alignments: Performs both pairwise and multiple protein structure alignments.
• Sequence and structure alignments: Automatically generates sequence alignments alongside structure alignments.
• PDB coordinates and RMSD statistics: Outputs PDB coordinates and root-mean-square deviation (RMSD) statistics for assessed superpositions.
• Difference distance plots: Produces difference distance plots to quantify positional deviations between superimposed structures.
• Static and interactive images: Generates static and interactive images of superimposed molecules for visualization of structural variations.
• Robust handling of structural variability: Handles structures that vary significantly in sequence, size, or shape.

Scientific Applications:

• Comparative Structural Analysis: Provides alignments, RMSD metrics, and visualizations to support comparative studies of protein structures.
• Analysis of structurally diverse proteins: Supports analysis of structurally divergent proteins and a wide range of superposition queries.

Methodology:

SuperPose utilizes a modified quaternion eigenvalue approach to perform pairwise and multiple protein structure superpositions, enabling handling of structures that vary significantly in sequence, size, or shape.