Constraint Based Approach to the Protein Folding Problem

Abstract
  • Bioinformatics is a challenging research area where every major contribution can have significant impact on medicine, agriculture, and industry.
  • Among various problems tackled in this area we are mainly interested in the problem of the prediction of the spatial shape of a polymer, given the sequence of monomers constituting it.
  • This problem can be naturally formalized using constraints over finite domains or intervals of reals.
 The problem
  • A protein can be seen as a linked list of aminoacids.
  • There are 20 kinds of aminoacids.
  • Each spatial, 3D, conformation of the linked list is associated to a given potential.
  • The problem is that of predicting the spatial conformation that will be reached by the protein that is (should be) the one minimizing the potential.
  • Two main aproaches: working within a discrete lattice, and working off-lattice.
  • A survey of our work: Logic Programming Techniques in Protein Structure Determination: Methodologies and Results. In Proc. of LPNMR09, Potsdam, Germany.

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     Alessandro Dal Palù      Agostino Dovier.
     Federico Fogolari.        Enrico Pontelli.     

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