Grid generation 1-3
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
MD simulation 1-2
Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom […]
Ligand alignment
Ligand alignment in LiveDesign Ligand alignment on a template structure using Shape screening. The workflow is exported as Computational model in […]
Substructure 1
Search a set of structures against a sketched query molecule or SMARTS patterns. Report the compounds that don't pass all the REOS filters. [Requires: […]
Batch execution 2
Test running the current workflow with KNIME_batch.py.
Run PyMOL 1-2
[Version: 6.8 Requires: Maestro, PyMOL Keywords: PyMOL, visualization]
Output column structure
Illustrate the Output column structure options (output only, input plus output, and output replaces input). The workflow also demonstrates a potential […]
Validate parameters 1-2
Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare the results using an […]