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Sliding Box Docking: a new stand-alone tool for managing docking-based virtual screening along the DNA helix axis



Andrelly Martins-José



Departamento de Química, Universidade Federal de Minas Gerais. Belo Horizonte, MG, Brazil. Av. Pres. Antônio Carlos, 6627. Pampulha, 31.270-901


Email; *Corresponding author


Article Type




Received July 08, 2013; Accepted July 09, 2013; Published August 07, 2013



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.



Binaries are freely available at



DNA, Docking tools, software, docking manager



José, Bioinformation 9(14): 750-751 (2013)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.