Similarity 1
Find the most similar compounds to a sketched molecule in a database. Screen the same database against several query structures. [Requires: Canvas]
Conformer cluster
Cluster conformers based on Cartesian or torsional RMSD. [Requires: Maestro, ConfGen]
GroupBy 1-2
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: […]
Docking 1-3
Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a […]
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 […]
QM Conformational search 1-2
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
Batch execution 2
Test running the current workflow with KNIME_batch.py.
Ligand alignment
Ligand alignment in LiveDesign Ligand alignment on a template structure using Shape screening. The workflow is exported as Computational model in […]
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 […]
MM Conformational search 1-2
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]