Constraint Logic Programming approach to protein structure prediction

Background: The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems. Results: Constraint Logic Programming techniques have been applied to the protein structure prediction problem on the face-centered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, Constraint Logic Programming on the face-centered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test implementation their (known) secondary structure and the presence...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Alessandro Dal Palù, Agostino Dovier, Federico Fogolari
• Keywords: BMCBI 2004, Constraint Logic Programming, Protein Structure Prediction, Structure Prediction Problem