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PLANTS configuration generator

KNIME nodes for PLANTS version 0.3.5.v201906271043 by Netherlands eScience Center

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

Icon
Input table

Output Ports

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Table with added PLANTS configuration column

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install KNIME PLANTS extension from the following update site:

KNIME 4.3

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Developers

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