Two constraint-based tools for protein folding

Introduction. A protein is a list of linked units called aminoacids. There are 20 different kinds of aminoacids and the typical length of a protein is less than 500 units. The Protein Structure Prediction Problem (PSP) is the problem of predicting the 3D native conformation of a protein, when its aminoacid sequence is known. The process for reaching this state is called the protein folding. It is widely accepted that the native conformation ensures a state of minimum free energy [1]. We assume some energy functions previously defined and we focus on the problem of finding the 3D conformation that minimizes them. We present two tools developed following different approaches to this problem. In the first we use Constraint Logic Programming over finite domains applied on the modeling of the Protein Structure Prediction problem on the Face-Centered Cubic Lattice [4]. In the second we develop a high-level off-lattice simulation method which makes use of Concurrent Constraint Programming [3]. The two codes are available at http://www.dimi.uniud.it/dovier/PF.