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 […]
Group looper
Illustrate how to iterate over structures in the input table with two different looper implementations. Extract the second lowest energy conformer of each […]
FEP analysis 1
An overview (predictions along with the ligand 2D structures) of a set of single edge FEP calculations is given as well as analysis details (including […]
Clustering 1
Cluster structures by fingerprints and inspect the clustering statistics to choose a good number of clusters. Create automatically the optimum number of […]
Run PyMOL 1
[Version: 6.8 Requires: Maestro, PyMOL Keywords: PyMOL, visualization]
Jobcontrol 1
The Jobcontrol node can be used to list the currently and recently run jobs, display information on these jobs, list and inspect the corresponding files. It […]
05_Multiple Sequence Viewer
[Version: 3.0.0 Requires: only the free node plugin and a Maestro installation for some workflows]
Conformer cluster
Cluster conformers based on Cartesian or torsional RMSD. [Requires: Maestro, ConfGen]
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 […]