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
This node was developed by Vernalis Research. For feedback and more information, please contact email@example.com
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)
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.
To use this node in KNIME, install the extension Vernalis KNIME Nodes from the below update site following our NodePit Product and Node Installation Guide:
A zipped version of the software site can be downloaded here.
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 firstname.lastname@example.org, 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.