Grid generation 1
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Watermap 1
A Watermap job is submitted and the map inspected in Maestro. It could be run on several complexes in one run.
Tools
Extract the atom-level properties to list the PDB conversion problems. [Requires: -] See other workflow examples using the Extract atom/bond […]
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 […]
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 […]
Shape screening 1-3
Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. Screen against several queries. Commands to run the […]
MCSS 1-4
Maximum Common Substructure Search (MCS): Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list […]
Python script 1-2
The Python Script nodes are used to extract ring properties, run a Macromodel conformational search with specific parameters, and measure distances between […]
Induced-fit docking 1-2
Run the default Induced Fit Docking protocol or customize the individual stages. The visual representation of the protein-ligand complexes (molecular […]
Conformer cluster
Cluster conformers based on Cartesian or torsional RMSD. [Requires: Maestro, ConfGen]