Bioluminate 1
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 […]
Reactive protein residues
Reactive protein residues are listed and compared for a set of structures. They are also highlighted when inspecting the structures. [Requires: […]
Grid generation 1-3
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Output column structure
Illustrate the Output column structure options (output only, input plus output, and output replaces input). The workflow also demonstrates a potential […]
Python script 1
The Python Script nodes are used to extract ring properties, run a Macromodel conformational search with specific parameters, and measure distances between […]
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 […]
Virtual screening 1-3
Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using different Glide modes (HTVS, […]
MM Conformational search 1
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
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 […]