Align pharmacophores

Align the query pharmacophores to the reference pharmacophore. This node computes the aligned query pharmacophore, the transformation matrix and Root-mean-square deviation (RMSD).

Algorithm:

Find pairs probe and reference points that are same type and are not too far apart.
Find biggest clique of pairs, using BronKerbosch clique detection algorithm .
Calculate optimal translation and rotation using Kabsch algorithm for all the found cliques.
Calculate RMSD and aligned pharmacophore based on points in each clique.

Options

Query Pharmacophore column (table 1): The input column of table 1 with Query Pharmacophores to be aligned.
Reference Pharmacophore: The reference Pharmacophore to base the alignment on.

Advanced Options

Cutoff: Tolerance threshold for considering two distances to be equivalent
Break num cliques: Break when set number of cliques is found
Cliques to align: Number of cliques of each query pharmacophore to align. Increasing this number will produce alignments of smaller cliques and cliques with less types.

Input Ports

: The table with pharmacophores to be aligned.

Output Ports

: Aligned pharmacophores with transformation matrix, RMSD, clique index and size of clique.

Views

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Workflows

3D-e-Chem extension testKNIME Hub

Developers

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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:

v5.9

Plugin provider: Netherlands eScience Center

Plugin version: 1.0.5.v202507210712

On NodePit since: 2025-12-11

Last update: 2026-01-06

KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, 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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