02_Run Maestro, Run Maestro command
[Version: 3.0.0 Requires: only the free node plugin and a Maestro installation for some workflows]
Epik
Predict ligand states with Epik and report the ionization form matrix. Generate with LigPrep minimized ionization-tautomeric forms ready to be […]
Docking 1-2
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 […]
Run PyMOL 1-2
Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]
Workbench nodes
Most commonly used workbench nodes. [Requires: -]
Jobcontrol 1-2
The Jobcontrol node can be used to list the currently and recently run jobs, display information on these jobs, list and inspect the corresponding files. It […]
Binding Pose Metadynamics
Various binding configurations of a single ligand in a single binding site are ranked.
Shape screening 1-4
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 […]
GroupBy 1
Illustrate how to use the GroupBy node in the context of the ionization form prediction over a range of pH. Various aggregation methods are used: […]
Missing Loop Refinement
Refine all the loops that were added using 'Fill loops' option in the Protein Preparation node and then compare it with initial stucture.