Installation test
Installation check in LiveDesign Basic test and installation checking The workflow is exported as Computational model in LiveDesign. TAGS: LiveDesign
QM Conformational search 1-3
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
QM properties
Calculate molecular orbitals and vibrational frequencies. [Requires: Ligprep, Jaguar] [Keywords: quantum mechanics, semi-empirical, parameter flow […]
Tools
Extract the atom-level properties to list the PDB conversion problems. [Requires: -] See other workflow examples using the Extract atom/bond […]
Binding site 1
Identify and characterize possible ligand binding sites (allosteric sites). Generate the ligand Interaction Diagrams. [Requires: SiteMap] The SiteMap […]
Run PyMOL 1-2
[Version: 6.8 Requires: Maestro, PyMOL Keywords: PyMOL, visualization]
02_Run Maestro, Run Maestro command
[Version: 3.0.0 Requires: only the free node plugin and a Maestro installation for some workflows]
Database preparation 1
Label compounds from a single vendor. Prepare and filter compounds by various criteria. Based on: Clark, D.E.; Higgs, C.; Wren, S.P.; Dyke, H.J.; Wong, M.; […]
Split multimers 1
Split protein multimers by chain ID and align binding sites. [Requires: Maestro]
MD simulation 1-3
Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom […]