KNIME-Maestro connector
Uses the KNIME-Maestro connector (replacing the Run Maestro 1:1 metanode) to alter some structures in the middle of a workflow, pick residues to sample in a […]
ESP 1
Run a semi-empirical and a Jaguar optimization job. Display the ligand ESP charges in Maestro. [Requires: LigPrep, Jaguar]
QM Conformational search 1
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
P450 SOM
In this workflow P450 Site of Metabolism calculation can be set and run to evaluate a set of ligands for the likely sites of metabolism by 2D6 or 2C9 P450 […]
MCSS 1-4
Maximum Common Substructure Search (MCS): Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list […]
Protocol workflow
This workflow is used in the LiveDesign protocol. [Requires: LiveDesign]
Grid generation 1-3
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Tautomer prediction
Generate the lowest energy tautomers or conformers (or both) for a set of structures, with optional protonation or deprotonation. It ensures that the […]
Shape screening 1-2
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 […]
Node Epik
[Version: 2.9.0] [Requires: Epik, LigPrep]