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: […]
Bioisoster replacement
Functional groups are replaced with bioisosteres that are available in the literature. [Requires: Maestro]
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 […]
Reactive protein residues
Reactive protein residues are listed and compared for a set of structures. They are also highlighted when inspecting the structures. [Requires: […]
Ligand alignment MD refinement 1
A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime […]
Loop over parameters
Dock the same set of ligands with several sets of docking parameters and compare the number of top scoring poses. [Requires: Glide]
Parameter flow variables 1-2
Use the parameter flow variables to control command-line options not exposed in the configuration panel. This is illustrated for the protein preparation, […]
Compare confo search methods
Run a conformational search with various methods and compare the lowest energy conformers. Parse the log file to extract relevant information. [Requires: […]