IconCovalent docking 

Dock and covalently binds ligands to the specified reactive residue in the protein target using Michael addition reaction type. [Requires: ProteinPrep, […]

IconMCSS 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 […]

IconDatabase 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.; […]

IconLigand alignment 

Ligand alignment in LiveDesign Ligand alignment on a template structure using Shape screening. The workflow is exported as Computational model in […]

IconRun PyMOL 1-2 

Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]

IconUnique 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]

IconLigand 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 […]

IconDocking 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 […]