HERMES

Comprehensive Protein Visualiser

• SuperStar
• Relibase+
• GOLD Suite

• The ability to view protein and ligand structures from external files
• Easy navigation of the protein structure and control of what is displayed
• A selection of visualisation options including a choice of display styles, colours, labelling schemes, and the ability to hide and then re-display atoms, residues, ligands, water molecules, etc
• Functionality to generate auxiliary objects such as centroids and ribbons
• The ability to restrict the contents of the rendered image based on the Z coordinate of individual objects (i.e. apply Z-clipping)
• The ability to measure and display distances, angles and torsion angles
• The option to find and display hydrogen bonds and non-bonded clashes, and to customise how they are defined geometrically
• Various display output options (e.g. png, jpg, bmp)
• The ability to edit ligands either manually or automatically to Cambridge Structural Database (CSD) conventions
• Stereoviewing functionality
• The ability to define and calculate descriptors
• Links to a pre-computed library of ligand geometries (Mogul)*
• Links to a precomputed library of non-bonded interactions (IsoStar)*
• * CSD System subscribers only

• Protonation of raw PDB files
• Easy navigation and modification of loaded SuperStar maps

Validation of a docking pose, using Hermes' link to Mogul: Mogul has identified a suspicious torsion (highlighted in ball and stick). Closer inspection of the histogram shows that although most observations are found around 90 degrees, the 7 degree angle (red line in the histogram) in the docked ligand is not unprecedented.