title: Sliding Box Docking: a new stand-alone tool for managing docking-based virtual screening along the DNA helix axis.
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.
  
  
  BACKGROUND
  Binaries are freely available at https://sourceforge.net/projects/slidingboxdocki.
authors: Departamento de Química, Universidade Federal de Minas Gerais. Belo Horizonte, MG, Brazil. Av. Pres. Antônio Carlos, 6627. Pampulha, 31.270-901.
authors: Andrelly
authors: A
authors: Martins-José
keywords: DNA; Docking tools; docking manager; software
references: Biophys J. 2005 Jan;88(1):404-11
references: 15516529
references: J Comput Chem. 2010 Jan 30;31(2):455-61
references: 19499576
references: Nucleic Acids Res. 1995 Sep 11;23(17):3385-92
references: 7567447
references: Biopolymers. 1997;44(3):201-15
references: 9591476