Protein Folding Simulation in CCP

A protein is identified by a finite sequence of aminoacids, each of them chosen from a set of 20 elements. The Protein Structure Prediction Problem is the problem of predicting the 3D native conformation of a protein, when its sequence of aminoacids is known. This problem is fundamental for biological and pharmaceutical research. Due to intrinsic computational limits, no general solution is available. In particular, simulation-based techniques that handle every chemical interaction between all atoms in the aminoacids (and the solvent) involve a huge number of computations. As a consequence, simulation programs of this family run extremely slow. Moreover, these programs are typically written in imperative languages and hard to be parallelized. In this paper we present a novel high-level simulation approach to the problem using concurrent constraint programming. Each aminoacid in the input sequence is viewed as a process that communicates with the others. The framework allows a modular representation of the problem and it is easily extensible for further refinements. The implementation in Mozart is rather natural; the code is intrinsically concurrent and thus easy to be parallelized.