Node Run Maestro
Automate some rendering preparation and inspect structures in Maestro. Select residues interactively in Maestro and use this selection to build an […]
Binding site 1-2
Identify and characterize possible ligand binding sites (allosteric sites). Generate the ligand Interaction Diagrams. [Requires: SiteMap] The SiteMap […]
Run PyMOL 1-2
[Version: 6.8 Requires: Maestro, PyMOL Keywords: PyMOL, visualization]
GroupBy 1
Illustrate how to use the GroupBy node in the context of the ionization form prediction over a range of pH. Various aggregation methods are used: […]
FEP analysis 2
An overview (predictions along with the ligand 2D structures) of a set of single edge FEP calculations is given as well as analysis details (including […]
Batch execution 2
Test running the current workflow with KNIME_batch.py.
Job control
Schrodinger Job control
Protein model building
Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid is generated and the binding site is […]
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.; […]