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Five Years of the KNIME Vernalis Cheminformatics Community Contribution

Author(s):

Stephen Roughley*   Pages 1 - 27 ( 27 )

Abstract:


Since the official release as a KNIME Community Contribution in June 2013, the Vernalis KNIME nodes have increased from a single node (the ‘PDB Connector’ node) to around 126 nodes (November 2017; Version 1.12.0); furthermore, a number of nodes have been adopted into the core KNIME product. In this review, we provide a brief timeline of the development of the current public release and an overview of the current nodes. We will focus in more detail on three particular areas: nodes accessing publicly available information via web services, nodes providing cheminformatics functionality without recourse to a cheminformatics toolkit, and nodes using one of the cheminformatics toolkits present in KNIME. We will conclude with a number of case studies demonstrating the use of KNIME at Vernalis.

Keywords:

KNIME Community Contribution, Cheminformatics, Matched Molecular Pairs (MMP, MMPA), Protein Data Bank (PDB), Sequences, Fingerprints, SMILES, Principal Moments of Inertia (PMI).

Affiliation:

Department of Chemistry & Cheminformatics, Vernalis Research Ltd, Granta Park, Great Abington, Cambridge CB21 6GB



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