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 […]
KNIME-Maestro connector
[Version: 7.5 Requires: (Prime) Keyworkds: Maestro commands, scripting]
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 […]
Database preparation 1-2
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.; […]
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 […]
Bioisoster replacement
Functional groups are replaced with bioisosteres that are available in the literature. [Requires: Maestro]
Ligand alignment
Ligand alignment in LiveDesign Ligand alignment on a template structure using Shape screening. The workflow is exported as Computational model in […]
Job control
Schrodinger Job control
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, […]
LiveDesign 1-3
Structures and properties are retrieved from LiveDesign. New properties are added to an existing Live report. [Products: LiveDesign]