Run PyMOL 1-2
Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]
MCSS 1-2
Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list the compounds that aren't included in this […]
Python script 1
The Python Script nodes are used to extract ring properties, run a Macromodel conformational search with specific parameters, and measure distances between […]
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 […]
Watermap 1
A Watermap job is submitted and the map inspected in Maestro. It could be run on several complexes in one run.
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.; […]
Docking 1-3
Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a […]
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 […]
ADME
ADME in LiveDesign ADME properties are calculated with QikProp. The workflow is exported as Computational model in LiveDesign. TAGS: […]
Clustering 1-4
Cluster structures by fingerprints and inspect the clustering statistics to choose a good number of clusters. Create automatically the optimum number of […]