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 […]
Readers and Writers
Read and write structure files. Read a list of PDB files from a directory. [Requires: Maestro] See also: - Docking - Grid generation: Glide grid […]
Induced-fit docking 1-2
Run the default Induced Fit Docking protocol or customize the individual stages. The visual representation of the protein-ligand complexes (molecular […]
Run PyMOL 1
Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]
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 […]
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 […]
Binding Pose Metadynamics
Various binding configurations of a single ligand in a single binding site are ranked.
KNIME-Maestro connector
[Version: 7.5 Requires: (Prime) Keyworkds: Maestro commands, scripting]