TeachOpenCADD-KNIME v1.0.0
Dominique Sydow, Michele Wichmann, Jaime Rodrı́guez-Guerra, Daria Goldmann, Gregory A. Landrum, Andrea Volkamer · Figshare · 2019
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