Loop over parameters
Dock the same set of ligands with several sets of docking parameters and compare the number of top scoring poses. [Requires: Glide]
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 […]
Batch execution 2
Test running the current workflow with KNIME_batch.py.
Compare confo search methods
Run a conformational search with various methods and compare the lowest energy conformers. Parse the log file to extract relevant information. [Requires: […]
Bioisoster replacement
Functional groups are replaced with bioisosteres that are available in the literature. [Requires: Maestro]
R group enumeration
Create libraries by substituting one or several attachments on a core structure with fragments from reagent compounds. Unique identifiers are assigned to […]
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.; […]
Validate parameters 1-3
Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare the results using an […]
Induced-fit docking 1-2
Run the default Induced Fit Docking protocol or customize the individual stages. The visual representation of the protein-ligand complexes (molecular […]