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Automated Matched Pairs

Erlwood Knime Open Source Cheminformatics version 4.0.0.v202012071342 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

: Data with RDKit molecules, IDs and property values

Output Ports

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

Best Friends (Incoming)

RDKit From Molecule (20 %)
SDF Reader (9 %)
RDKit Descriptor Calculation (8 %) Streamable
RDKit Fingerprint (6 %) Streamable
Free-Wilson Matched Pairs (4 %)
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Best Friends (Outgoing)

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Row Filter (7 %) Streamable
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Installation

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

KNIME 4.3

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

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Developers

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