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 […]
Shape screening 1-3
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 […]
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]
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 […]
Induced-fit docking 1
Run the default Induced Fit Docking protocol or customize the individual stages. The visual representation of the protein-ligand complexes (molecular […]
Validate parameters 1-2
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 […]
Substructure 1-2
Search a set of structures against a sketched query molecule or SMARTS patterns. Report the compounds that don't pass all the REOS filters. [Requires: […]
Cocrystallized ligand redocking 1
Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized […]
MM Conformational search 1-2
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
Conformer cluster
Cluster conformers based on Cartesian or torsional RMSD. [Requires: Maestro, ConfGen]