Computational investigations of folded self-avoiding walks related to protein folding

Jacques Bahi (1) , Christophe Guyeux (1) , Kamel Mazouzi (2) , Laurent Philippe (1)

1 FEMTO-ST - Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174)
2 MESOCENTRE - Mésocentre de calcul

Various subsets of self-avoiding walks naturally appear when investigating existing methods designed to predict the 3D conformation of a protein of interest. Two such subsets, namely the folded and the unfoldable self-avoiding walks, are studied computationally in this article. We show that these two sets are equal and correspond to the whole n-step self-avoiding walks for n 14, but that they are different for numerous n 108, which are common protein lengths. Concrete counterexamples are provided and the computational methods used to discover them are completely detailed. A tool for studying these subsets of walks related to both pivot moves and protein conformations is finally presented.

Domaines: Calcul parallèle, distribué et partagé [cs.DC]; Cryptographie et sécurité [cs.CR]; Modélisation et simulation

Jacques Bahi, Christophe Guyeux, Kamel Mazouzi, Laurent Philippe. Computational investigations of folded self-avoiding walks related to protein folding. Journal of Bioinformatics and Computational Biology, 2013, 47, pp.246--256. ⟨10.1016/j.compbiolchem.2013.10.001⟩. ⟨hal-00932017⟩