SEM

SEM generates symmetry-equivalent three-dimensional (3D) molecular structures for proteins and nucleic acids to analyze molecular symmetry and conformational diversity.

Key Features:

• Symmetry-equivalent generation: Produces multiple symmetry-equivalent conformations from an input 3D molecular structure.
• Input from PDB: Accepts atomic coordinates derived from Protein Data Bank (PDB) entries determined by X-ray crystallography.
• Molecule types: Operates on proteins and nucleic acids.
• Visualization: Renders reference structures and generated symmetric equivalents using the RasMol graphics program.
• Coordinate export: Exports atomic coordinates of generated symmetry-equivalent molecules.

Scientific Applications:

• Structural biology: Facilitates exploration of molecular symmetry and conformational diversity in structural biology and bioinformatics.
• Protein function analysis: Aids analysis of protein conformational variation relevant to protein function.
• Interaction studies: Supports biomolecular interaction studies by providing alternative symmetry-related conformers for interface analysis.
• Drug design: Assists drug design by enabling assessment of symmetry-related binding geometries.
• Behavior prediction: Enables evaluation of how proteins might behave or interact under different conditions based on symmetry-related structures.

Methodology:

Generates multiple symmetry-equivalent conformations from input atomic coordinates (PDB entries determined by X-ray crystallography) and renders reference and symmetric equivalents with RasMol; generated atomic coordinates can be exported.