Validate parameters 1
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 […]
Group looper
Illustrate how to iterate over structures in the input table with two different looper implementations. Extract the second lowest energy conformer of each […]
Virtual screening 1-3
Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using different Glide modes (HTVS, […]
Maestro commands - highlight residues
HIghlight and label residues selected on a list. [Requires: Maestro]
Build antibody 2
Several antibody models are built using Bioluminate starting from the heavy and light chain sequences. Sequences can be read from an XLS spreadsheet. […]
Semiempirical
Run semi-empirical NDDO quantum chemical optimization and generate surface properties [Requires: Maestro, LigPrep]
Loop over parameters
Dock the same set of ligands with several sets of docking parameters and compare the number of top scoring poses. [Requires: Glide]
Sitemap and docking
Prepare a set of PDB structures and identify possible binding sites with Sitemap. Generate receptor grids with Glide for each site and used to dock […]
Parameter flow variables 1
Use the parameter flow variables to control command-line options not exposed in the configuration panel. This is illustrated for the protein preparation, […]
Cocrystallized ligand redocking 1
Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized […]