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PLANTS configuration generator

Node to generate a PLANTS configuration.

Source code for PLANTS node is available on GitHub .

Options

Search algorithm

Search speed: Search speed setting

Binding site

Center X: X coordinate of binding site sphere
Center Y: Y coordinate of binding site sphere
Center Z: Z coordinate of binding site sphere
Radius: Radius of binding site sphere

Cluster algorithm

RMSD similarity threshold: RMSD similarity threshold for cluster algorithm
Number of structures: Number of structures generated by the cluster algorithm

Scoring functions

Scoring function: Radius of binding site sphere

Input

Protein file: Protein file in MOL2 file format
Ligand file: Ligand file file in MOL2 file format

Output

Directory: Output directory
Protein conformations: Protein conformations
Protein binding site: Protein binding site
Protein splitted: Fixed and dynamic parts of protein in separate files
Multi-mol2: Multi-mol2
Ranked soft links: Ranked soft links
Merged protein: Merged protein

Input Ports

: Input table

Output Ports

: Table with added PLANTS configuration column

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Installation

To use this node in KNIME, install the extension 3D-e-Chem KNIME nodes from the below update site following our NodePit Product and Node Installation Guide:

v5.2

A zipped version of the software site can be downloaded here.

Plugin provider: Netherlands eScience Center

Plugin version: 0.3.6.v202311221207

On NodePit since: 2023-12-06

Last update: 2024-12-18

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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