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Current Medicinal Chemistry

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ISSN (Print): 0929-8673
ISSN (Online): 1875-533X

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Review Article

Five Years of the KNIME Vernalis Cheminformatics Community Contribution

Author(s): Stephen D. Roughley*

Volume 27, Issue 38, 2020

Page: [6495 - 6522] Pages: 28

DOI: 10.2174/0929867325666180904113616

open access plus

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).

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