Scaling Up

Folding abstract proteins in a three-dimensional lattice is all very well and good for proving polynomial time convergence, but that doesn't provide us with a practical system for predicting protein structure. The system that follows my thesis prototype will have to accomodate the properties and problems inherent in folding real-world proteins with the following enhancements:

• Space-filling amino acid residues which interact mechanically
• Model Van der Wals force and electromechanical properties
• Folding by Ramachandran angles
• Fold within real-valued polar coordinate system

Additonal Folding Enhancements

Although not a part of tertiary folding, the following enhancements will be needed to further simulate real-world proteins.

• Quertenary folding
• Promoters
• Post-translation modifications

Genetic Algorithm Enhancements

There are also several genetic algorithm issues to be addressed:

• Termination
• Protein Pathways