Protonation forms
Protonation forms in LiveDesign Generate protonation forms with Epik and populates the LiveReport with the structure of the most probable form in a new […]
Protein Alignment
Extract one monomer from each of the two multimers. Align the binding sites (via the 'Align Binding Sites' node) or the whole structure (using the 'Protein […]
Virtual screening 1-3
Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using different Glide modes (HTVS, […]
Batch execution 2
Test running the current workflow with KNIME_batch.py.
Maestro commands - highlight residues
HIghlight and label residues selected on a list. [Requires: Maestro]
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 […]
Split multimers 1
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
KNIME Server - QikProp
Workflow to be run on a KNIME server and invoked from a LiveDesign Computational model. [Requires: LigPrep, QikProp]
Binding site 1
Identify and characterize possible ligand binding sites (allosteric sites). Generate the ligand Interaction Diagrams. [Requires: SiteMap] The SiteMap […]
QM Conformational search 1-3
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]