DeprecatedVernalis Chemistry Matched-Molecular Pairs extension for KNIME Workbench version 1.12.0.v201708101336 by Vernalis (R&D), UK
This node pre-filters molecules by viabilty in the specified MMP schema. The user can specify the number of cuts to be made (1 - 10), and whether Hydrogens should be added (for 1 cut only).
A variety of fragmentation options are included:
Guidelines for Custom rSMARTS Definition
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 " (http://www.rdkit.org/docs/Overview.html#the-contrib-directory) (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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