IconFEP 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 […]

IconMM Conformational search 1 

Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]

Icon01_​Chemistry external tool 

The Chemistry external tool nodes can be used to parse a log file with basic shell commands or run any command line utilities. Quick form nodes can be used […]

IconMD 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 […]

IconProtein model building 

Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid is generated and the binding site is […]

IconGroup looper 

Illustrate how to iterate over structures in the input table with two different looper implementations. Extract the second lowest energy conformer of each […]

IconMissing Loop Refinement 

Refine all the loops that were added using 'Fill loops' option in the Protein Preparation node and then compare it with initial stucture.

IconJobcontrol 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 […]

IconMM Conformational search 1-4 

Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]