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 […]
Run PyMOL 1-2
[Version: 6.8 Requires: Maestro, PyMOL Keywords: PyMOL, visualization]
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 […]
R group enumeration
Create libraries by substituting one or several attachments on a core structure with fragments from reagent compounds. Unique identifiers are assigned to […]
Docking 1-3
Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a […]
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 […]
QM Conformational search 1
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
Maestro commands - highlight residues
HIghlight and label residues selected on a list. [Requires: Maestro]