DeprecatedVernalis Chemistry Matched-Molecular Pairs extension for KNIME Workbench version 1.27.0.v202008190633 by Vernalis (R&D), UK
This node implements the Hussain and Rea algorithm (Ref 1) for finding Matched Molecular Pairs in a dataset. The user can specify the number maximum number of cuts to be made (1 - 10), and whether Hydrogens should be added (1 cut only). All cuts from 1 to the specified number are made.
The node implements the molecule fragmentation part of the process, 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.
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 fragment key
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 KNIME Nodes from the following update site:
You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.
Do you have feedback, questions, comments about NodePit, want to support this platform, or want your own nodes or workflows listed here as well? Do you think, the search results could be improved or something is missing? Then please get in touch! Alternatively, you can send us an email to email@example.com, follow @NodePit on Twitter, or chat on Gitter!
Please note that this is only about NodePit. We do not provide general support for KNIME — please use the KNIME forums instead.