The secondary and tertiary structure of a protein is related to chemical characterisitics of the individual amino acid residues, but a clear picture of the secondary structure may not be apparent for one protein sequence alone. Comparing many aligned, related sequences can reveal patterns of sequence conservation that indicate the location of residues essential for the function, folding or solubility of the protein. The rules are manipulated as corresponding combinations of commands to predict specific properties.
Users can easily extend or create new rules for their specific purposes.
Bioinformatics 16, 950-951. Pattern recognition and self-correcting distance geometry calculations applied to myohemerythrin. FEBS Letter 34, 147-153. Predicting the helix packing of globular proteins by self-correcting distance geometry. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules.