Automated Matched Pairs


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.

Input Ports

  1. Type: Data
    Data with RDKit molecules, IDs and property values

Output Ports

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


This node is part of the extension

Erlwood Knime Open Source Cheminformatics


Short Link

Drag node into KNIME Analytics Platform