On the Complexity of Protein Local Structure Alignment Under the Discrete Fr\'echet Distance

Abstract

We show that given $m$ proteins (or protein backbones, which are modeled as 3D polygonal chains each of length O(n)) the problem of protein local structure alignment under the discrete Fr\'{e}chet distance is as hard as Independent Set. So the problem does not admit any approximation of factor $n^{1-\epsilon}$. This is the strongest negative result regarding the protein local structure alignment problem. On the other hand, if $m$ is a constant, then the problem can be solved in polygnomial time.