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 […]
Validate parameters 1-2
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 […]
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 […]
Python script 1-2
The Python Script nodes are used to extract ring properties, run a Macromodel conformational search with specific parameters, and measure distances between […]
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 […]
LiveDesign 1
Structures and properties are retrieved from Live Design. New properties are added to an existing Live report. [Products: Live Design]
Run PyMOL 1
[Version: 6.8 Requires: Maestro, PyMOL Keywords: PyMOL, visualization]
Similarity 1-2
Find the most similar compounds to a sketched molecule in a database. Screen the same database against several query structures. [Requires: Canvas]
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 […]