AutoDock

AutoDock

AutoDock is the first docking package to model the ligand with full conformational flexibility. AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Over the years, it has been modified and improved to add new functionalities, and multiple engines have been developed.

The package consists of two sequentially applied programs, AutoGrid and AutoDock.

AutoGrid is initially used to calculate the noncovalent energy of interaction between the rigid part of the receptor and a probe atom that is located at various grid points of the lattice. Furthermore,  AutoGrid generates an electrostatic potential grid map and a desolvation map.

The full set of grid maps and the flexible part of the receptor are used by AutoDock to guide the docking process of the selected ligands.

 

AutoDock's main strengths are

(i)                          receptor flexibility

(ii)                        blind-docking

(iii)                     precalculated grid maps on a binding site

(iv)                     free-energy scoring function based on linear regression analysis, the AMBER force field, and a large set of protein–ligand complexes with known inhibition constants

(v)                        good correlation between predicted inhibition constants and experimental data.

It is available at http://autodock.scripps.edu/.

Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina.

AutoDock 4 actually consists of two main programs: autodock performs the docking of the ligand to a set of grids describing the target protein; autogrid pre-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.

AutoDock Vina does not require choosing atom types and pre-calculating grid maps for them. Instead, it calculates the grids internally, for the atom types that are needed, and it does this virtually instantly. A graphical user interface called AutoDockTools, or ADT  helps to set up which bonds will treated as rotatable in the ligand and to analyze dockings.

 

AutoDock has applications in:

  • X-ray crystallography;
  • structure-based drug design;
  • lead optimization;
  • virtual screening (HTS);
  • combinatorial library design;
  • protein-protein docking;
  • chemical mechanism studies

 

 


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