StreamableVernalis Chemistry Matched-Molecular Pairs extension for KNIME Workbench version 1.27.2.v202010191232 by Vernalis (R&D), UK
This node implements the molecule fragmentation part of the Hussain and Rea algorithm (Ref 1) for finding Matched Molecular Pairs in a dataset, enabling the fragmented molecule key-value pairs to be stored in a database for later recall or used directly in a subsequent pair-finding node. The user can specify the number of cuts to be made (1 - 10), and whether Hydrogens should be added (1 cut only)
A variety of fragmentation options are included:
Guidelines for Custom (r)SMARTS Definition
An rSMARTS is no longer required, but may be specified if preferred for backwards compatibility. If specified must comply with the following rules. Otherwise, simply a match for two atoms separated by a single, acyclic bond must be provided
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')
4. N. M. O'Boyle, J. Bostrom, R. A. Sayle and A. Gill, "Using Matched Molecular Series as a Predictive Tool To Optimize Biological Activity", J. Med. Chem., 2014, 57, 2704-2713 (DOI:10.1021/jm500022q)
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