Exploiting Model Checking in Constraint-based Approaches to the Protein Folding.

Abstract

In this paper we show how model checking can be used to drive the solution search in the protein folding problem encoded as a constraint optimization problem. The application of the model checking technique allows us to distinguish between meaningful protein conformations and bad ones. This classification of conformations can then be exploited by constraint solvers to significatively prune the search space of the protein folding problem. Furthermore, our approach seems promising in the study of folding/energy landscapes of proteins.