DeprecatedVernalis Chemistry Matched-Molecular Pairs extension for KNIME Workbench version 1.18.1.v201812201431 by Vernalis (R&D), UK
This node implements the Hussain and Rea algorithm for finding Matched Molecular Pairs in a dataset (See Ref. 1). The user can specify the number of cuts to be made (1 - 10), and whether Hydrogens should be added.
A variety of fragmentation options are included:
Guidelines for Custom rSMARTS Definition
Optionally, when only a single cut is made, or connectivity tracking is enabled, context-fingerprints can be generated (one for each attachment point). The fingerprints generated are RDKit Morgan fingerprints, rooted at the attachment point(s) of the unchanging portion
The algorithm is implemented using the RDKit toolkit.
1.J. Hussain and C Rea, " Computationally efficient algorithm to identify matched molecular pairs (MMPs) in large datasets ", J. Chem. Inf. Model. , 2010, 50 , 339-348 (DOI: 10.1021/ci900450m ).
2. S. D. Roughley and A. M. Jordan " The Medicinal Chemist’s Toolbox: An Analysis of Reactions Used in the Pursuit of Drug Candidates ", J. Med. Chem. , 2011, 54 , 3451-3479 (DOI: 10.1021/jm200187y )
3. G. Landrum " An Overview of RDKit " (section entitled 'mmpa')
To use this node in KNIME, install Vernalis Chemistry Matched-Molecular Pairs extension for KNIME Workbench from the following update site:
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