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 […]
Jobcontrol 1
The Jobcontrol node can be used to list the currently and recently run jobs, display information on these jobs, list and inspect the corresponding files. It […]
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 […]
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.
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 […]
Split multimers 1-3
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
Build antibody 1
Several antibody models are built using Bioluminate starting from the heavy and light chain sequences. Sequences can be read from an XLS spreadsheet. […]
Diversity
Pick diverse molecules from a library and inspect the structures. [Requires: Canvas]
KNIME-Maestro connector
Uses the KNIME-Maestro connector (replacing the Run Maestro 1:1 metanode) to alter some structures in the middle of a workflow, pick residues to sample in a […]