Node Workbench nodes
Most commonly used workbench nodes. [Version: 3.0.0] [Requires: -]
Protocol workflow
This workflow is used in the LiveDesign protocol. [Requires: LiveDesign]
Node Run Maestro
Automate some rendering preparation and inspect structures in Maestro. Select residues interactively in Maestro and use this selection to build 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 […]
Split multimers 1-3
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
QM Conformational search 1-3
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
Build antibody 1
Several antibody models are built using Bioluminate starting from the heavy and light chain sequences. Sequences can be read from an XLS spreadsheet. […]
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 […]
GroupBy 1-2
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: […]