Epik
Predict ligand states with Epik and report the ionization form matrix. Generate with LigPrep minimized ionization-tautomeric forms ready to be […]
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] […]
ADME
ADME in LiveDesign ADME properties are calculated with QikProp. The workflow is exported as Computational model in LiveDesign. TAGS: […]
Watermap 2
A Watermap job is submitted and the map inspected in Maestro. It could be run on several complexes in one run.
Ensemble docking
Dock ligands into multiple conformations of the binding site and report the best pose per ligand. [Requires: Glide]
Database analysis 1-2
Assess the coverage of a database from the distribution of the distance to the nearest neighbor of each molecule in the database. List the three most […]
Grid generation 1
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
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 […]
Shape screening 1-2
Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. Screen against several queries. Commands to run the […]
Random forest
Random forest in LiveDesign Property prediction with a Random forest QSAR model. The workflow is exported as Computational model in […]