TeachOpenCADD-KNIME v1.0.3
Dominique Sydow, Michele Wichmann, Jaime Rodrı́guez-Guerra, Daria Goldmann, Gregory A. Landrum, Andrea Volkamer · Figshare · 2021
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.1.0.3) contains the following changes: Contains updated version of full workflow pipeline (TeachOpenCADD.knar) but also individual workflows (TeachOpenCADD-WorkflowX_XXX.knar) W1-W8: Replace deprecated TeachOpenCADD tutorials GH link with website link W1-W8: Where applicable, replace deprecated nodes with their latest version, e.g. CSV Reader/Writer, Concatenate, Table Row to Variable W1: Update local copy of query results (data/W1_query_results_20210125.table) W1: Increase GET Request timeout from 30s to 100s (otherwise only parts of the ChEMBL dataset could be downloaded) W8: Replace PDB query workflow completely due to new RCSB PDB API (old PDB KNIME nodes did not work any more) - new PDB workflow created by Greg Landrum W8 (Get structures from PDB, filter/sort and select top 4): Fixed bug - outdated output PDB structures were updated according to W8 changes in v1.0.1 by updating execution of last workflow node