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AutoDock 4

LigandScout Extensions for the KNIME Workbench version 1.7.9 by InteLigand GmbH

The AutoDock 4 node enables docking experiments via AutoDock 4.

Options

Settings

Genetic algorithm runs
Defines the specified number of docking runs using the simulated annealing search engine.
(Default: 20)
RMSD cluster tolerance
Set the RMSD threshold (in Å) for joining together multiple docking results and show them as one entry in the list of docked poses.
(Default: 2)
Number of individuals on population
Defines the size of the initial population for the genetic algorithm search.
(Default: 150)
Max. number of energy evaluations
Set the maximum number of energy evaluations performed during each genetic algorithm search run.
(Default: 2 500 000)
Max. number of generations
Set the maximum number of generations simulated during each genetic algorithm search run.
(Default: 27 000)

Active Site Selection

All active sites for which the node should consider the docking process.
(Default: The biggest active site)

Input Ports

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Table containing the macromolecule(s)
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Table containing the molecule(s) to dock

Output Ports

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Table containing the docking result(s)

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install LigandScout Extensions for the KNIME Workbench from the following update site:

KNIME 4.3

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Developers

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