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Automated Matched Pairs

Erlwood Knime Open Source Cheminformatics version 4.0.0.qualifier by Erlwood

This node detects and outputs all the possible matched molecular pairs in a data set and returns the pairs, along with the corresponding (single-point) chemical transformations and property changes. Requires the RDKit nodes.

Because it is not based on MCS detection, the algorithm comparatively fast and efficient. More details can be found here:

1. Wagener, M. and Lommerse, J.P.M. (2006). "The quest for bioisosteric replacements". Journal of Chemical Information and Modeling, 46 (2), 677-685.

2. Hussain, J. and Rea, C. (2010). "Computationally efficient algorithm to identify matched molecular pairs (MMPs) in large data sets". Journal of Chemical Information and Modeling, 50 (3), 339-348.

3. Papadatos, G. et al. (2010). "Lead optimization using matched molecular pairs: Inclusion of contextual information for enhanced prediction of hERG inhibition, solubility, and lipophilicity". Journal of Chemical Information and Modeling, 50 (10), 1872-1886.

Options

RDKit molecule column
The column that contains the RDKit molecules.
ID column
The column that contains the IDs or names of the molecules
Property column
The column that contains the (measured) property values of the molecules (e.g. activity)

Input Ports

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Data with RDKit molecules, IDs and property values

Output Ports

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Table containing matched pairs (left (L) and right (R)), transformation, context (=common substructure), property change, MCS distance and transformation atom count
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Network adjacency matrix

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install Erlwood Knime Open Source Cheminformatics from the following update site:

KNIME 4.2

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

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Developers

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