Jaguar pKa
Evaluate the pKa of specified atoms using Jaguar. [Requires: Ligprep, Jaguar] [Keywords: Quantum mechanics, pKa, parameter flow variables]
KNIME-Maestro connector
[Version: 7.5 Requires: (Prime) Keyworkds: Maestro commands, scripting]
Protein model building
Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid is generated and the binding site is […]
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 […]
Jobcontrol 1
The Jobcontrol node can be used to list the currently and recently run jobs, display information on these jobs, list and inspect the corresponding files. It […]
Sitemap and docking
Prepare a set of PDB structures and identify possible binding sites with Sitemap. Generate receptor grids with Glide for each site and used to dock […]
Node Epik
[Version: 2.9.0] [Requires: Epik, LigPrep]
ESP 1-2
Run a semi-empirical and a Jaguar optimization job. Display the ligand ESP charges in Maestro. [Requires: LigPrep, Jaguar]
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 […]
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 […]