Abstract
Sliding Box Docking is a program that manages simulations of ligand docking at different defined positions of a three-dimensional DNA structure. The procedure is similar to inverse docking, which is a method that performs docking simulations of a single ligand in the active sites of different targets. Sliding Box Docking manages docking simulations of one ligand into a box that slides along the DNA helix axis in regular steps. For each box position a score is calculated using the separate Autodock Vina software, and the results are automatically plotted. The evaluation of ligand interaction at different DNA locations can highlight the specificity of ligands for different DNA- sequences. When assessing the affinity between ligans AT base pairs, results for docking simulations with a test set that included berenil, distamycin, hoechst 33258, and netropsin were as expected, agreeing well with affinities previously described in the literature. AVAILABILITY: Binaries are freely available at https://sourceforge.net/projects/slidingboxdocki.