View, Analyse and Explore Macromolecular Structures and Their Properties with Hermes

Visualize proteins, DNA, and other macromolecules with or without bound ligands shown (e.g. docking poses or observed ligands) and generate high-definition images or animations. Analyse systems further with CSD-Discovery, to perform docking, generate conformers, overlay ligands, and more.


Comprehensive, interactive visualization

Show your work with clear, visual presentation. Choose from standard styles or create your own, customize the display and annotations to show what matters to you. Generate high-resolution images and animations of macromolecules.

Customize and display specific feature

Fully custom visualization. Show ribbons, sheets, ligands, metals, waters, and more to highlight and communicate your findings.

Access advanced analysis tools

Track changes to know when repository script edits were made and specifically what they were. Track back to how the data was generated — see the exact settings used in each analysis.

Get started easily

Complete your analysis in Hermes, with CSD-Discovery access advanced tools to perform docking, analyse interactions, generate conformers, overlay ligands and more. Hermes is the desktop interface method to access GOLD, our validated and trusted protein-ligand docking algorithm.

Overlay molecular structures

Perform structural superimposition of multiple conformations of the same protein or other macromolecules, access the root-mean-square (RMS) to deeply understand similarities and differences between the structures.

Explore published or proprietary structures

Apply all these features to published or new structures — Hermes can open many common file formats including .mol2 .mol .pdb and .sdf

Included in
  • CSD-Core
  • CSD-Enterprise
  • Academic Research
  • Agrochemical
  • Pharmaceutical Software
Use Cases
  • End-to-End Molecular Design
  • Search Known Small Molecules
Using the GOLD software for protein ligand docking on a laptop

How to Navigate through Hermes

Learn how to:

– Prepare protein or small molecule structures.

– Show protein structures in ribbon.

– Analyse binding sites in protein-ligand structures.


Hermes supports a range of molecular structure files for macromolecules, including .pdb, .ent, .mol, .mol2 and many more.

See a full and up-to-date list of file types Hermes supports here.

You can customize the view to show ribbons, sheets, ligands, metals, waters and more, with the option to add annotations for features like hydrogen bond length, or amino acid labels. Styles and colours can also be customized to best convey your work and share your findings.

Yes — if you have a suitable licence, including academic licences, analytical tools within CSD-Discovery are accessible in Hermes. See the full range of tools available for academics in our free or paid versions of CSD software, and for commercial users in different packages.