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 […]
Binding site 1-2
Identify and characterize possible ligand binding sites (allosteric sites). Generate the ligand Interaction Diagrams. [Requires: SiteMap] The SiteMap […]
05_Multiple Sequence Viewer
[Version: 3.0.0 Requires: only the free node plugin and a Maestro installation for some workflows]
Shape screening 1-5
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 Conformer cluster
[Version: 2.9.0] [Requires: Maestro, (ConfGen)]
Library design workshop
Bioisostere and R-group enumeration using custom or predefined isosteres and libraries. Reaction-Based Enumeration to rapidly generate idea molecules with […]
Batch execution 1
Test running the current workflow with KNIME_batch.py.
Ensemble docking
Ensemble docking in LiveDesign Ensemble docking in 2 binding site conformations and the best scoring conformation is reported along with the […]
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.; […]
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 […]