Database preparation 1
Label compounds from a single vendor. Prepare and filter compounds by various criteria. Based on: Clark, D.E.; Higgs, C.; Wren, S.P.; Dyke, H.J.; Wong, M.; […]
KNIME-Maestro connector
[Version: 7.5 Requires: (Prime) Keyworkds: Maestro commands, scripting]
Induced-fit docking 1
Run the default Induced Fit Docking protocol or customize the individual stages. The visual representation of the protein-ligand complexes (molecular […]
Tools
Extract the atom-level properties to list the PDB conversion problems. [Requires: -] See other workflow examples using the Extract atom/bond […]
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 […]
Job control
Schrodinger Job control
LiveDesign 1
Structures and properties are retrieved from Live Design. New properties are added to an existing Live report. [Products: Live Design]
FEP analysis 2
An overview (predictions along with the ligand 2D structures) of a set of single edge FEP calculations is given as well as analysis details (including […]
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 […]