0 ×

Structure-based Pharmacophore Creator

LigandScout Extensions for the KNIME Workbench version 1.7.9 by InteLigand GmbH

The Structure-based Pharmacophore Creator node generates structure-based pharmacophores from given macromolecule-ligand complexes.

Options

Active Site Selection

All active sites for which the node should generate a structure-based pharmacophore.
(Default: All active sites found)

Advanced Settings

Minimum number of chemical features
Generated pharmacophore models containing less chemical features will be discarded and not included in the output table.
(Default: 3)
Interaction cutoff threshold
Defines a sphere surrounding each non-hydrogen atom of the ligand. All non-hydrogen atoms in the environment which are within this sphere are considered as possible interaction partners during the pharmacophore generation process.
(Default: 7 Å)
Surface accessibility threshold
Defines the minimum sterical accessability threshold for moieties to be considered as hydrophobic. The higher the threshold the more restrictive the feature identification will be.
(Default: 0.250)
Add Exclusion Volumes Coat
Adds an exclusion volumes coat that represents the binding pocket size is used.
(Default: disabled)
Include Environment
Additionally outputs the ligand environment.
Default: disabled)
Remove Water
Removes the water molecules before the pharmacophopre generation.
(Default: disabled)
Remove Ions
Removes the metal ions before the pharmacophopre generation.
(Default: disabled)

Metal Binding

Maximum binding direction deviation
Defines the maximum angle deviation from a ligating atoms idealized metal-binding axis. Lowering the value causes more restrictive handling of preferred binding direction deviations.
(Default: 120.00°)
Maximum binding symmetry deviation
Defines the maximum allowed relative binding length difference of a metal atom to two or more ligating atoms. This setting is only effective in case of chelating moieties like hydroxamates. The lower the value the more restrictive is the handling.
(Default: 0.75°)

Steric Constraints

Alpha C distance
Set the minimum and maximum distance, such that an excluded volume on an alpha carbon can be generated. If the alpha carbon has interactions with ligand atoms closer than the maximum distance and no other feature is closer than the minimum distance, then an excluded volume will be created on an alpha carbon.
(Default: Min: 2.0 Å; Max: 4.0 Å)
Alpha C exclusion tolerance
Sets the tolerance value which an excluded volume on an alpha carbon will have.
(Default: 1.00 Å)

Hydrogen Bonding

sp2
For an sp2 hydrogen bond donor atom. The angle between the vector (hbd atom, hydrogen) and vector (hydrogen, hba atom) must be below this threshold to be a valid hydrogen bond.
(Default: 50.00°)
sp3
For an sp hydrogen bond donor atom. The angle between the vector (hbd atom, hydrogen) and vector (hydrogen, hba atom) must be below this threshold to be a valid hydrogen bond.
(Default: 34.00°)
Acceptor
Calculate the weighted vector from the hydrogen bond acceptor atom to all of its neighbors. This mixed direction vector is inverted and checked against the vector (hydrogen bond acceptor atom, hydrogen bond donor atom). This angle must be below the specified threshold.
(Default: 85.00°)

Aromatic Interactions

Orthogonal center deviation
The minimum and maximum distance constraint two orthogonal plane feature center points (one from the core and the other from the environment) must meet.
(Default: Min: 0.0 Å; Max: 2.0 Å)
Parallel center deviation
The minimum and maximum distance constraint two parallel plane feature center points (one from the core and the other from the environment) must meet.
(Default: Min: 0.0 Å; Max: 2.0 Å)
Angle tolerance for pi-cation interactions
The angle constraint that must be met for the angle between vector (plane center, ion position) and plane normal vector to be a valid plane ion interaction feature.
(Default: 60.00°)
Angle tolerance for pi-pi interactions
Orthogonal sets the maximum angle the two normal vectors for two pi-pi orthogonal plane features may enclose to be a valid interaction. Parallel sets the maximum angle the two normal vectors for two Pi-Pi parallel plane features may enclose to be a valid interaction.
(Default: orthogonal: 20.00°; parallel: 20.00°)

Halogen Bonding

Distance tolerance
Set the distance tolerance.
(Default: 0.3 Å)
Bond angle
Set the bond angle tolerance.
(Default: 140.00°)
Acceptor angle
Set the acceptor bond angle tolerance.
(Default: 90.00°)
MET Exclusion angle
Set the MET exclusion angle.
(Default: 10.00°)

Input Ports

Icon
Table containing the macromolecule-ligand complexe(s)

Output Ports

Icon
Table containing the pharmacophore-model(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

You don't know what to do with this link? Read our NodePit Product and Node Installation Guide that explains you in detail how to install nodes to your KNIME Analytics Platform.

Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform. Browse NodePit from within KNIME, install nodes with just one click and share your workflows with NodePit Space.

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.