The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound

The protein structure prediction problem is one of the most (if not the most) important problem in computational biology. This problem consists of finding the conformation of a protein with minimal energy. Because of the complexity of this problem, simplified models like Dill's HP-lattice model [15], [16] have become a major tool for investigating general properties of protein folding. Even for this simplified model, the structure prediction problem has been shown to be NP-complete [5], [7]. We describe a constraint formulation of the HP-model structure prediction problem, and present the basic constraints and search strategy. Of course, the simple formulation would not lead to an efficient algorithm. We therefore describe redundant constraints to prune the search tree. Furthermore, we need bounding function for the energy of an HP-protein. We introduce a new lower bound based on partial knowledge about the final conformation (namely the distribution of H-monomers to layers).