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

Abstract

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 proteins conformations is finally presented.

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References in corpus (2)

• Protein structure prediction software generate two different sets of conformations. Or the study of unfolded self-avoiding walks
• Is protein folding problem really a NP-complete one ? First investigations