Covalent docking
Dock and covalently binds ligands to the specified reactive residue in the protein target using Michael addition reaction type. [Requires: ProteinPrep, […]
MCSS 1-3
Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list the compounds that aren't included in this […]
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.; […]
Job control
Schrodinger Job control
Ligand alignment
Ligand alignment in LiveDesign Ligand alignment on a template structure using Shape screening. The workflow is exported as Computational model in […]
Run PyMOL 1-2
Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]
Unique molecule titles
Ensure unique molecule titles (using the KNIME RowID or the Schrödinger dedicated node). This is useful in the context of Canvas. [Requires: Maestro, Canvas]
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 […]
Docking 1-3
Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a […]