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:

  1. Find pairs probe and reference points that are same type and are not too far apart.
  2. Find biggest clique of pairs, using BronKerbosch clique detection algorithm .
  3. Calculate optimal translation and rotation using Kabsch algorithm for all the found cliques.
  4. 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

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The table with pharmacophores to be aligned.

Output Ports

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

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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: 1.0.5.v202311211458
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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