Protocol workflow
This workflow is used in the LiveDesign protocol. [Requires: LiveDesign]
Watermap 2
A Watermap job is submitted and the map inspected in Maestro. It could be run on several complexes in one run.
Multiple Sequence Viewer
Opens the Multiple Sequence Viewer panel to visualize sequences or edit an alignement. [Requires: Maestro]
QM descriptors
It generates a series of jobs and harvests molecular (including Dipole Moment, HOMO/LUMO, isodensity surface contributions, Internal energy, energy […]
Cocrystallized ligand redocking 2
Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized […]
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 […]
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 […]
Maestro commands
The Run maestro command node is used to alter the formal charge of some atoms defined by an ASL and for altering the structure rendering before inspection […]
Shape screening 1-2
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 […]
Protein model building
Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid is generated and the binding site is […]