Similarity 1-2
Find the most similar compounds to a sketched molecule in a database. Screen the same database against several query structures. [Requires: Canvas]
Reactive protein residues
Reactive protein residues are listed and compared for a set of structures. They are also highlighted when inspecting the structures. [Requires: […]
Bioluminate 1-2
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 […]
Output column structure
Illustrate the Output column structure options (output only, input plus output, and output replaces input). The workflow also demonstrates a potential […]
Protocol workflow
This workflow is used in the LiveDesign protocol. [Requires: LiveDesign]
Bioisoster replacement
Functional groups are replaced with bioisosteres that are available in the literature. [Requires: Maestro]
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 […]
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 […]
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.; […]
Docking 1
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 […]