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 […]
Ligand alignment MD refinement 2
A Desmond molecular dynamics simulation is run on each ligand prealigned in the protein binding site. Then the representative frames are refined with Prime […]
Run Maestro, command
Automate some rendering preparation and inspect structures in Maestro. Select residues interactively in Maestro and use this selection to build an […]
KNIME-Maestro connector
[Version: 7.5 Requires: (Prime) Keyworkds: Maestro commands, scripting]
LiveDesign 1
Structures and properties are retrieved from Live Design. New properties are added to an existing Live report. [Products: Live Design]
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 […]
Node MSV
[Version: 2.9.0] [Requires: Maestro]
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 […]
Epik
Predict ligand states with Epik and report the ionization form matrix. Generate with LigPrep minimized ionization-tautomeric forms ready to be […]
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 […]