Instant structure visualization with Mol* Viewer
Modern structural workflows are no longer confined to a single desktop or a single file. Models are generated in pipelines, shared across teams, and revisited as new evidence comes in.
Yet for many researchers, “visualizing a structure” still means downloading files to a laptop, moving data between systems, or launching a remote desktop session. If you work on shared infrastructure or in large project directories, it can also mean running a job on a cluster just to start a graphical tool. None of that is ideal when you simply want to open a model quickly, inspect it, and move on.
To remove that friction, the VIB Data Core now supports Mol* Viewer, a modern, web-based, open-source toolkit for visualizing and analyzing macromolecular structure data. Mol* (pronounced “mol-star”) is developed by the PDBe, RCSB, CEITEC and ELIXIR CZ teams and runs entirely in the browser. In other words: no local installs, no remote desktops, no downloads required.
What Mol* Viewer enables at VIB
Mol* Viewer makes it possible to open structural files directly from VIB Data Core Compute Storage. If your files are already on the cluster storage, you can simply point Mol* to the directory and start exploring.
That means:
- No downloads of potentially large structure files or associated outputs
- No SLURM jobs just to visualize a result
- No detours through local machines or manual file transfers
This is especially useful in workflows where structure files are produced or refined on shared infrastructure, for example, prediction runs, docking campaigns, model refinement, or pipelines that generate many candidate structures that must be triaged quickly.
Mol* Viewer is valuable to anyone working with macromolecular structures at VIB, including:
- Structural biologists inspecting predicted or experimental models (proteins, complexes, nucleic acids)
- Computational biologists and bioinformaticians working with structure outputs from pipelines and automated workflows
- AI/ML users reviewing protein structure predictions, variants, and model quality checks (e.g., iterative evaluation of model outputs)
- Drug discovery and molecular interaction researchers doing rapid inspection of binding sites, conformations, or structure-based hypotheses
- Core facility users and collaborators who need an easy way to review results without setting up software environments
Because it runs in the browser, Mol* is also practical for quick sharing and discussion: teams can review structures in a meeting setting without everyone needing the same local software stack.
“A web viewer might sound like a small convenience, until you’re working at scale,” says Rafael Buono, Team lead Compute at the VIB Data Core. “In many modern projects, structures are not single files but batches of outputs generated by pipelines. Researchers may need to open dozens or hundreds of structures to filter candidates, compare conformations, or spot artifacts. In those cases, eliminating repetitive steps (download, move, launch) can meaningfully improve velocity.”
There is also a data governance and reproducibility angle. If structure files live in a managed storage environment, keeping inspection “close to where the data lives” reduces the proliferation of duplicate files across personal laptops and ad-hoc folders.
“It’s an important step toward cleaner research practice: fewer copies, fewer mismatched versions, and clearer provenance.”
About Mol*: an open standard in the community
Mol* is not a niche tool. It is maintained by two of the world’s central structure-data organizations—PDBe and RCSB PDB—and has become a widely used tool for web-based structural visualization. It supports common structure formats and provides interactive features for exploring macromolecules directly in a modern browser.
“Choosing a viewer isn’t just about rendering structures,” says Bert Droesbeke, who integrated Mol* Viewer into the VIB Data Core environment via Open OnDemand. “We needed something researchers already recognize and trust, that’s actively maintained by the community, and that we can run entirely in the browser without local installs. Mol* checked those boxes, and it also gave us the right hooks to integrate it cleanly with our environment, including a file picker that lets users open models straight from Compute Storage.”
The expertise network of ELIXIR Europe played a key enabling role by connecting the VIB Data Core and Mol* teams, explains Rafael: “This is another example of how ELIXIR works as a network for sharing skills, knowledge and practical, real-world solutions for researchers.”
“By adopting Mol* Viewer in VIB’s infrastructure, we align with a toolset that is open-source, actively maintained by leading community institutions, and designed for modern, interactive, web-based workflows.”
How to get started
If your structural files are already on VIB Data Core Compute Storage, Mol* Viewer can open them directly. If you’re not yet using Compute Storage for your structural data, the Data Core team can help you move or organize it efficiently.
Interested in using Mol* Viewer for your work, or want to know which file types and paths are supported? Reach out to the VIB Data Core team and we’ll help you get set up.
