volkamerlab

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Published October 7, 2019 | Version v1.0.2
Lesson Open

TeachOpenCADD-KNIME v1.0.2

Authors/Creators

  • 1. In Silico Toxicology, Institute of Physiology, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
  • 2. KNIME GmbH, Körtestr. 10, 10967 Berlin, Germany
  • 3. KNIME AG, Technoparkstr. 1, 8005 Zurich, Switzerland

Description

TeachOpenCADD-KNIME: a teaching platform for computer-aided drug design using KNIME workflows

TeachOpenCADD is a teaching platform for cheminformatics and structural bioinformatics. Central topics in computer-aided drug design (CADD) are covered in two different material formats:

  • GUI-based KNIME workflows (https://hub.knime.com/volkamerlab/space/TeachOpenCADD/)
  • Code-based Jupyter Notebooks (https://github.com/volkamerlab/TeachOpenCADD)

The TeachOpenCADD KNIME pipeline consists of eight inter-connected workflows (W1-8), each containing one topic in CADD. The pipeline is illustrated using the epidermal growth factor receptor (EGFR), but can easily be applied to other targets of interest.

Topics include:

  • W1: Data acquisition from ChEMBL
  • W2: Molecular filtering: ADME and lead-likeness criteria
  • W3: Molecular filtering: Unwanted substructures
  • W4: Ligand-based screening: Compound similarity
  • W5: Compound clustering
  • W6: Maximum common substructures
  • W7: Ligand-based screening: Machine learning
  • W8: Protein data acquisition: Protein Data Bank

This release (v.1.0.2) contains the following change:

  • W8 (Get structures from PDB, filter/sort and select top 4): Fixed bug - outdated output PDB structures were updated according to W8 changes in v1.0.1 by updating execution of last workflow node

Files

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Additional details

Related works

Is cited by
Journal article: 10.1021/acs.jcim.9b00662 (DOI)

References

  • Sydow D, Wichmann M, Rodríguez-Guerra J, Goldmann D, Landrum G, Volkamer A (2019). TeachOpenCADD-KNIME: A teaching platform for computer-aided drug design using KNIME workflows. JCIM, 10.1021/acs.jcim.9b00662