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Resources2023-07-17T10:18:55+01:00

Publications

Our scientists are influential world figures in fragment and structure-based drug discovery, speaking regularly at major conferences and with many widely cited publications, some of which are listed below.

Enabling organometallic libraries by flow: A tale of two metals
A covalent fragment-based strategy targeting a novel cysteine to inhibit activity of mutant EGFR kinase
PAC-FragmentDEL – photoactivated covalent capture of DNA-encoded fragments for hit discovery
Design and Synthesis of Pyrrolo[2,3‑d]pyrimidine-Derived Leucine-Rich Repeat Kinase 2 (LRRK2) Inhibitors Using a Checkpoint Kinase 1 (CHK1)-Derived Crystallographic Surrogate
Fragment-Derived Selective Inhibitors of Dual-Specificity Kinases DYRK1A and DYRK1B
Structure-Guided Discovery of Potent and Selective DYRK1A Inhibitors
Fragment-Based Discovery of Novel non-Hydroxamate LpxC Inhibitors with Antibacterial Activity
Discovery of S64315, a Potent and Selective Mcl-1 Inhibitor
Five Years of the KNIME Vernalis Cheminformatics Community Contribution

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Software

Vernalis uses a range of commercial and open source software.  We also contribute open source software to the wider community.  In addition to our KNIME community contribution, our developers have also made contributions to a number of open source projects including the RDKit, DataWarrior, FXMolViewer, OpenBabel and BioJava.

We have been KNIME Trusted Community contributors since June 2013.  The ‘trusted’ status provides guarantees about testing, security, maintenance and backwards compatibility to ensure our nodes are suitable for use in a production environment.  A more detailed description of our nodes can be found at the Vernalis Community Contribution Homepage, the KNIME Hub, and also via the Node Pit website.  We have recently published a historical overview of the development of the contribution to December 2017 (Roughley, Curr. Med. Chem. 2020).

Broadly speaking, the nodes fall into three categories:

  • General utility nodes – nodes of use to the wider KNIME community, beyond the cheminformatics arena. The nodes include many flow control nodes (switches, loop start / end nodes), fingerprint manipulation nodes, collection modifying nodes, database nodes, and a variety of testing and benchmarking nodes.
  • Data access nodes – our original node was the PDB Connector, developed with Enspiral Discovery, which allows advanced query of the RCSB PDB. Following changes to the RCSB RESTful webservices in 2020, we completely re-wrote this family of nodes and have added a variety of other nodes to query or download data from public sources.  We also provide a variety of nodes for loading text-based files into KNIME, in both plain-text, XML and chemical formats.
  • Cheminformatics and Structural Informatics nodes – nodes which allow extracting or processing data from PDB files, sequence data, and SMILES data (via the ‘Speedy SMILES’ nodes, which are designed for fast pre-processing of large SMILES-based datasets without internal or explicit conversion to a chemical toolkit format). We also provide nodes to perform Matched Molecular Pair Analysis (MMPA), and to calculate a range of molecular properties. Many of our nodes use the RDKit toolkit.  More recently, we have also added a small number of bioinformatics nodes.

Some of our nodes have been subsequently donated to KNIME and incorporated into the KNIME core product.

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