Constraint Logic Programming approach to protein structure prediction.docVIP

BMC Bioinformatics BioMedCentral Research article Open Access Constraint Logic Programming approach to protein structure prediction Alessandro Dal Palù1, Agostino Dovier*1 and Federico Fogolari2 Address: 1Dipartimento di Matematica e Informatica, Università di Udine. Via delle Scienze 206, 33100 Udine, Italy and 2Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, P.le Kolbe 4, 33100 Udine, Italy Email: Alessandro Dal Palù - dalpalu@dimi.uniud.it; Agostino Dovier* - dovier@dimi.uniud.it; Federico Fogolari - ffogolari@mail.dstb.uniud.it * Corresponding author Published: 30 November 2004 Received: 09 July 2004 Accepted: 30 November 2004 BMC Bioinformatics 2004, 5:186 doi:10.1186/1471-2105-5-186 This article is available from: /1471-2105/5/186 ? 2004 Dal Palù et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract 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