Vernalis Nodes for KNIME (trusted extension)

About the nodes

These nodes have been developed within the research group at Vernalis.  The functionality provided has been of use in our own fragment- and structure-based drug discovery work; and by releasing the nodes it is our hope that others may find them of use too.

The nodes fall into three general categories:

  1. Nodes that provide an interface within KNIME for interacting with certain public web services
  2. Nodes that work with cheminformatics file types or data types locally
  3. Utility nodes that provide some general functionality within KNIME

The Vernalis contribution has recently been described in an article in Curr. Med. Chem. "Five Years of the KNIME Vernalis Cheminformatics Community Contribution" (DOI: 10.2174/0929867325666180904113616)

The current list of node categories and nodes is shown below.  Clicking on a category heading takes you to the corresponding position in the detailed description page.

  • European PubMed Central
    • European PubMed Central Advanced Search
  • Flow Control
    • Flow Variable
      • Flow Variable IF Switch
      • Flow Variable IF Switch (Flow Variable Value)
      • Flow Variable End IF
      • Flow Variable CASE Switch
      • Flow Variable End CASE
    • Database
      • Database IF Switch
      • Database IF Switch (Flow Variable Value)
      • Database End IF
      • Database CASE Switch
      • Database End CASE
    • Loops
      • Timed Loops
        • Chunk Loop Run-for-time Loop Start
        • Chunk Loop Run-to-time Loop Start
        • Table Row To Variable Run-for-time Loop Start
        • Table Row To Variable Run-to-time Loop Start
        • Timed Loop End (1 port)
        • Timed Loop End (2 ports)
        • Timed Loop End (3 ports)
        • Timed Loop End (Upto 4 ports)
        • Variable Timed Loop End
      • Loop End (3 ports)
      • Loop End (upto 4 ports)
      • Loop End (upto 6 ports)
    • Delays
      • Wait-for-time
      • Wait-to-time
    • IF Switch (Flow Variable Value)
  • IO
    • Read Variables
    • Write Variables
  • Matched Molecular Pairs (MMPs)
    • Filtering
      • MMP Molecule Filter
      • MMP Molecule Splitter
    • Fragmentation
      • MMP Molecule Fragment (3rd Gen)
      • MMP Molecule Multi-cut Fragment (3rd Gen)
    • Pair Generation
      • Fragments to MMPs
    • MMP Calculate Maximum Cuts
    • MMP Fragmentation Type Loop Start
    • Uniquify IDs
  • Principal Moments of Inertia (PMIs)
    • Align to Inertial Principal Axes
    • PMI Calculation
  • RCSB PDB Tools
    • PDB Connector
    • PDB Connector (XML Query String)
    • PDB Downloader (Source)
    • PDB Downloader
  • Local PDB Tools
    • PDB Loader
    • PDB Saver
    • PDB Property Extractor
  • Sequence Tools
    • FASTA Sequence Extractor
    • PDB Sequence Extractor
  • Fingerprints
    • Fingerprint Properties
  • Miscellaneous
    • Text-based IO
      • Load text-based files
      • Save File Locally
    • List Folders
    • Random Numbers Generator
    • SMARTSViewer
  • Testing

    • Benchmarking
      • Benchmark Start
      • Benchmark Start (2 ports)
      • Benchmark Start (3 ports)
      • Benchmark End
      • Benchmark End (2 ports)
      • Benchmark End (3 ports)

A more detailed description of the nodes can be found here.

Any questions about the nodes can be posted on the Vernalis KNIME forum, or sent to the developers by e-mail.  We currently have a number of unreleased nodes at various stages of development – so if you don’t see what you need, please ask!

Examples

Some simple example workflows can be found on the KNIME Public server, which can be accessed from the KNIME Explorer menu in KNIME Desktop.  Once you have logged-in as guest, please look for 099_Community/11_Vernalis.

Installing the nodes

As a Trusted Community Contribution, you may find that you already have access to the stable version of the Vernalis KNIME nodes!  If not, or for further information on installing either the stable release or the very latest features (but not guaranteed stable), please see the KNIME Community Contributions page.

About Vernalis Research

We develop and apply fragment and structure-based methods to solve problems in drug discovery, and have generated cell-active lead compounds and development candidates against targets in oncology, neurodegeneration, anti-infectives and inflammation.

Our established group of experienced scientists is based at our fully-equipped research laboratories on Granta Park, Cambridge UK. We integrate fragment-based approaches, structural biology, biophysics, assay technology and molecular modelling with extensive medicinal chemistry expertise to enable drug discovery on both established and novel targets. We have the experience and capabilities for progressing projects from target identification through to clinical candidate. We have generated lead compounds on kinases, ATPases, protein-protein interactions and GPCRs, leading to clinical candidates for Chk1, Hsp90, Bcl-2, Mcl-1, FAAH and A2A.

We balance an internal portfolio of drug discovery projects with fully integrated collaborations on targets with pharmaceutical and academic partners. Our shared-risk approach ensures a high level of engagement from our scientists and rewards success. Current and recent disclosed collaborations include those with Servier, Daiichi Sankyo, Lundbeck, Genentech and Asahi Kasei Pharma.

Release Notes

Release notes and changelog can be found here.

Source Code

The source code can be accessed at https://anonymous:knime@community.knime.org/svn/nodes4knime/trunk/com.vernalis.

License

The Vernalis nodes are released under GPLv3.