AutoDock

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.

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.

Another software belonging to Autodock is a graphical user interface called AutoDockTools, or ADT for short, which amongst other things 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. 

 

AutoDock 4 is free and is available under the GNU General Public License. AutoDock Vina is available under the Apache license, allowing commercial and non-commercial use and redistribution. Please click on “http:/autodock.scripps.edu/” to see details.

AutoDock Vina

AutoDock Vina is a new generation of docking software from the Molecular Graphics Lab. It achieves significant improvements in the average accuracy of the binding mode predictions, while also being up to two orders of magnitude faster than AutoDock 4.1 

Because the scoring functions used by AutoDock 4 and AutoDock Vina are different and inexact, on any given problem, either program may provide a better result. AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. 

Detailed information and the software package can be found on the AutoDock Vina web site.

VMD

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer.

To get detailed information and the software package, please click on http://www.ks.uiuc.edu/Research/vmd/.

Pymol

A molecular visualization system on an open source foundation, maintained and distributed by Schrödinger. It is a powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures. Its multiple functions include: a) view 3D molecular structures, b) render figures artistically, c) animate molecules dynamically, d) export Pymol geometry, e) present 3D data with AxPyMOL, and e) develop with JyMOL.

To download the software and see more details， please tranfer to the access “http://www.pymol.org/pymol”。