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Biologic Software  
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Introduction


When the specific interaction of small molecules with selected targets is central for research, in silico approaches such as protein-ligand docking become important tools. AutoGrid/AutoDock (Morris et al., 1998) is one of the most popular software packages for docking. In this package, AutoGrid is used to calculate the non-covalent energy of interaction between the receptor and a probe atom that is located in the different grid points of a lattice that divides the receptor's area of interest (i.e. the area of the macromolecule where the possibility of ligand binding is studied). AutoGrid builds as many files as the number of probe atoms used and these probes are: (a) the atoms that will be present in the ligands that will be docked onto the receptor (thus generating the corresponding affinity grid maps); and (b) a point charge of +1 (an alternative method can also generate this electrostatic potential grid map using a Poisson-Boltzmann finite difference method as in DELPHI; Sharp et al., 1987). The next program in the package (i.e. AutoDock) uses the full set of grid maps built by AutoGrid to guide the docking process of the select ligands through the lattice volume. AutoGrid/AutoDock also has a graphic interface called AutoDockTools (ADT) that provides the user with powerful tools for analyzing the docking results and allows an easy set up of: (a) the macromolecule and ligand coordinates in the format required by AutoGrid/AutoDock; (b) the file needed to run AutoGrid around the receptor's area of interest (i.e. the so-called gpf file); and (c) the file needed for docking one specific ligand onto this area of the receptor (i.e. the so-called dpf file). While ADT has strongly decreased the learning-curve needed for using AutoGrid/AutoDock, it is also true that some docking tasks with this package, although possible, are far from trivial for users without strong computer skills. Examples of such tasks are: (a) using receptor flexibility during docking; (b) the automatic docking of a large library of ligands onto one or more receptors; and (c) docking a ligand library onto one or more receptors without defining one a priori ligand-binding site on them (the so-called "blind-docking" analysis) and using a short distance between grid points. To overcome these difficulties, we have developed BDT (Vaqué et al., 2006), a graphic front-end application that runs on top of four Fortran programs (i.e. make_grids, combine_grids, make_docks and analyze, one under each BDT window tab), which control the conditions of AutoGrid and AutoDock runs.

BDT is available for free, upon request, for non-commercial research.