Shape screening 1-4
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 […]
QM Conformational search 1
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
Database analysis 1
Assess the coverage of a database from the distribution of the distance to the nearest neighbor of each molecule in the database. List the three most […]
MCSS 1-3
Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list the compounds that aren't included in this […]
Database preparation 1-3
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 1-4
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
Missing Loop Refinement
Refine all the loops that were added using 'Fill loops' option in the Protein Preparation node and then compare it with initial stucture.
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]
Reaction-based enumeration
Enumerate structures by substitution of R groups in the reactants and products of a single- or multi-step reaction. It is also use for Core hopping.
Bioluminate 1-3
The antibody structure can be split into Fc, Fab and Fv domains. The node scans proteins for residues that are candidates for mutation and evaluate the […]