SymD

SymD detects internal symmetry in protein structures by identifying pseudo‑symmetry within single polypeptide chains through circular permutation and self‑alignment of structural coordinates.

Key Features:

• Internal symmetry detection: Identifies pseudo‑symmetry within single polypeptide chains in protein structures.
• Alignment scan procedure: Performs an alignment scan that circularly permutes one copy of the protein structure across residue offsets and aligns it to the original.
• Self‑alignment analysis: Aligns permuted and original structural copies to detect repeating units and symmetry relationships.
• Symmetry axis reporting: Provides detailed information about detected symmetry axes.
• Sequence alignment reporting: Reports sequence alignments both before and after applying symmetry transformations.

Scientific Applications:

• Structural characterization: Characterizing internal repeats and symmetric patterns in protein architecture.
• Functional inference: Inferring potential functional implications of internal pseudo‑symmetry.
• Protein modeling: Informing protein structure modeling and prediction by identifying symmetric constraints.
• Protein design and folding studies: Guiding design of symmetric proteins and investigation of protein folding mechanisms.

Methodology:

SymD performs an alignment scan that circularly permutes one copy of the protein structure by all possible residue offsets and aligns it to the original structure to identify symmetry and determine symmetry axes, and it reports sequence alignments before and after the symmetry transformations.