Using Secondary Structure Information for Protein Folding in CLP(FD)


The protein folding problem is the problem of predicting the 3D structure of a protein when the linear sequence of aminoacids identifying it is known. In this paper we present a declarative implementation in Constrain & Generate style in CLP(ℱFD) of the protein folding problem, for models based on face-centered cubes. We use information concerning secondary structure (and other heuristics) to sensibly prune the search space. Preliminary results on real proteins are encouraging.

11th International Workshop on Functional and (constraint) Logic Programming