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.; […]
Missing Loop Refinement
Refine all the loops that were added using 'Fill loops' option in the Protein Preparation node and then compare it with initial stucture.
Maestro commands - highlight residues
HIghlight and label residues selected on a list. [Requires: Maestro]
Jaguar pKa
Evaluate the pKa of specified atoms using Jaguar. [Requires: Ligprep, Jaguar] [Keywords: Quantum mechanics, pKa, parameter flow variables]
Cocrystallized ligand redocking 1
Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized […]
Ensemble docking
Dock ligands into multiple conformations of the binding site and report the best pose per ligand. [Requires: Glide]
Build antibody 2
Several antibody models are built using Bioluminate starting from the heavy and light chain sequences. Sequences can be read from an XLS spreadsheet. […]
MM Conformational search 1-3
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
Reaction-based enumeration
Enumerate structures by substitution of R groups in the reactants and products of a single- or multi-step reaction. It is also use for Core hopping.
Loop over parameters
Dock the same set of ligands with several sets of docking parameters and compare the number of top scoring poses. [Requires: Glide]