Semiempirical
Run semi-empirical NDDO quantum chemical optimization and generate surface properties [Requires: Maestro, LigPrep]
Shape screening 1-4
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 […]
Tools
Extract the atom-level properties to list the PDB conversion problems. [Requires: -] See other workflow examples using the Extract atom/bond […]
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] […]
Bioisosteres
Bioisosteres - in LiveDesign Replace functional groups of each LiveReport ligand with bioisosteres, generating all the single replacements. The […]
Run PyMOL 1
[Version: 6.8 Requires: Maestro, PyMOL Keywords: PyMOL, visualization]
QM Conformational search 1
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: […]
Library design workshop
Bioisostere and R-group enumeration using custom or predefined isosteres and libraries. Reaction-Based Enumeration to rapidly generate idea molecules with […]
Node Run Maestro
Automate some rendering preparation and inspect structures in Maestro. Select residues interactively in Maestro and use this selection to build an […]