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 […]
QM Conformational search 1-2
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
Split multimers 1-2
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
Related PDB structures
Related PDB structures PDB structures containing ligands similar to each LiveReport structures are listed. The PDB structure with the most similar ligand […]
Epik
Predict ligand states with Epik and report the ionization form matrix. Generate with LigPrep minimized ionization-tautomeric forms ready to be […]
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 […]
01_Chemistry external tool
The Chemistry external tool nodes can be used to parse a log file with basic shell commands or run any command line utilities. Quick form nodes can be used […]
FEP analysis 2
An overview (predictions along with the ligand 2D structures) of a set of single edge FEP calculations is given as well as analysis details (including […]
02_Run Maestro, Run Maestro command
[Version: 3.0.0 Requires: only the free node plugin and a Maestro installation for some workflows]
Cocrystallized ligand redocking 2
Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized […]