Difference between revisions of "Software:autodock"

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(Autodock)
 
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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.
 
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.
 
AutoDock 4 actually consists of two main programs:  
 
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.  
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* '''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. There also is a GUI called AutoDockTools (ADT), which amongst other things helps to set up which bonds will treated as rotatable in the ligand and to analyze dockings.
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* 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. There also is a GUI called AutoDockTools (ADT), which amongst other things helps to set up which bonds will treated as rotatable in the ligand and to analyze dockings.
  
  

Latest revision as of 17:16, 27 May 2016

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. 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. There also is a GUI called AutoDockTools (ADT), which amongst other things helps to set up which bonds will treated as rotatable in the ligand and to analyze dockings.