Ligand alignment MD refinement 2
A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime […]
Bioluminate 1-4
The antibody structure can be split into Fc, Fab and Fv domains. The node scans proteins for residues that are candidates for mutation and evaluate the […]
Node Workbench nodes
Most commonly used workbench nodes. [Version: 3.0.0] [Requires: -]
Substructure 1
Search a set of structures against a sketched query molecule or SMARTS patterns. Report the compounds that don't pass all the REOS filters. [Requires: […]
ESP 1
Run a semi-empirical and a Jaguar optimization job. Display the ligand ESP charges in Maestro. [Requires: LigPrep, Jaguar]
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 […]
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: […]
Reaction-based enumeration
Enumerate structures by substitution of R groups in the reactants and products of a single- or multi-step reaction. It is also use for Core hopping.
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.
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 […]