TeachOpenCADD-KNIME v1.0.4

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 (v1.0.4) contains the following changes - runs on KNIME 4.5:

Mainly update deprecated nodes - big thank you to Alice Krebs for her efforts on this new release!

• Workflow: TeachOpenCADD
  • Joiner (deprecated) (17)         Joiner (282)
  • Joiner (deprecated) (25)         Joiner (27)
  • Joiner (deprecated) (40)         Joiner (283)
  • Joiner (deprecated) (41)         Joiner (284)
  • Joiner (deprecated) (42)         Joiner (285)
  • Table Row to Variable (deprecated) (121)     Table Row to Variable (123)
  • Table Reader (deprecated) (265)       Table Reader (273)
  • Table Reader (deprecated) (269)       Table Reader (281)
  • CSV Reader (deprecated) (273)        CSV Reader (274)
  • Table Writer (deprecated) (268)         Table Writer (280)
  • String to Number (deprecated) (269) String to Number (274)
  • Table Row to Variable (deprecated) (61)       Table Row to Variable (62)
  • Sorter (29) - The Sorter node had to be introduced in order for the loop to run without major resettings
• Workflow: TeachOpenCADD_Workflow1_Data_acquisition_ChEMBL
  • Table Reader (deprecated) (265)       Table Reader (273)
  • Table Row to Variable (deprecated) (121)     Table Row to Variable (123)
  • String to Number (deprecated) (265) String to Number (274)
  • Variable to Table Row (deprecated) (61)       Variable to Table Row (62)
• Workflow: TeachOpenCADD_Workflow2_ADME_filter
  • No changes
• Workflow: TeachOpenCADD_Workflow3_Unwanted_substructures
  • No changes
• Workflow: TeachOpenCADD_Workflow4_Similarity_search
  • Joiner (deprecated) (40)         Joiner (283)
  • Joiner (deprecated) (41)         Joiner (284)
  • Joiner (deprecated) (42)         Joiner (285)
  • CSV Reader (deprecated) (273)        CSV Reader (274)
• Workflow: TeachOpenCADD_Workflow5_Compound_clustering
  • Table Writer (deprecated) (268)         Table Writer (280)
  • Column Filter (279)     Column Filter (279)
  • Joiner (deprecated) (17)         Joiner (282)
  • Joiner (deprecated) (25)         Joiner (27)
  • Table Reader (deprecated) (269)       Table Reader (281)
  • Sorter (29) - The Sorter node had to be introduced in order for the loop to run without major resettings
• Workflow: TeachOpenCADD_Workflow6_Maximum_common_substructure
  • No changes
• Workflow: TeachOpenCADD_Workflow7_Machine_learning
  • No changes
• Workflow: TeachOpenCADD_Workflow8_Data_acquisition_PDB
  • No changes