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 Workbench nodes
Most commonly used workbench nodes. [Version: 3.0.0] [Requires: -]
Run PyMOL 1
Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]
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 […]
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.; […]
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 […]
Ensemble docking
Ensemble docking in LiveDesign Ensemble docking in 2 binding site conformations and the best scoring conformation is reported along with the […]
GroupBy 1-2
Illustrate how to use the GroupBy node in the context of the ionization form prediction over a range of pH. Various aggregation methods are used: […]
MD simulation 1
Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom […]
KNIME server - Random forest
Workflow to be run on a KNIME server and invoked from a LiveDesign Computational model. [Requires: LigPrep, QikProp]