Here we present pyDockDNA, which is based on the pyDock program, with a new module for reading and parsing DNA molecules. The protocol is composed of two major steps: sampling and scoring. The first sampling step consists in the generation of 10,000 protein-DNA docking models by FTDock [5]. This program takes a protein and a nucleic acid coordinate file, discretizes the molecules into corresponding 3D grids, and computes their geometric correlation by using Fast Fourier Transform algorithms to speed up the translations between the two molecules.