One of the recurring challenges in molecular modeling is that integrating external tools and scripts often disrupts your workflow. Whether you rely on docking programs, simulation pipelines, or visualization utilities, switching between environments—coupled with writing tedious wrapper code—can slow down research and introduce unnecessary friction.
If this sounds familiar, you’re not alone. Many researchers find themselves reinventing the wheel just to run external tools alongside their molecular modeling work. That’s where SAMSON’s app infrastructure offers a helpful shift in perspective.
Streamlined integration with SAMSON Apps
SAMSON, the integrative platform for molecular design, includes a modular system called Apps to seamlessly bring external tools, custom code, or entirely new features into your working environment. From running docking protocols to connecting with remote services, Apps allow you to extend your workflow without writing code from scratch—or leaving the SAMSON interface.
SAMSON Apps are modular components that can:
- Serve as wrappers around third-party software tools like docking engines or quantum chemistry packages,
- Interface with external web services or executables,
- Offer entirely new features based on the SAMSON Application Programming Interface (API),
- Integrate legacy scripts or pipelines into the SAMSON environment.
In short, Apps act like bridges that connect your modeling work with external components, but without needing to build that bridge every time.
How to get started
You can explore available Apps by navigating to Home > Apps within the SAMSON interface. The platform already provides a set of default Apps, ranging from structure builders to simple analysis tools. But the real flexibility comes from SAMSON Connect, where you can browse and install additional Apps tailored to your research needs.
One popular example is the AutoDock Vina Extended App, which provides an integrated interface to set up and run docking calculations directly in SAMSON:
This App connects the widely-used AutoDock Vina engine to SAMSON’s visual interface, allowing you to define ligand-receptor interactions visually and preview results in real-time. Instead of running Vina as a command-line job and converting structure files repeatedly, you interact with your models directly in SAMSON—and the app handles the rest.
What if you want to make your own App?
If you have scripts or software components you frequently use, consider wrapping them as your own SAMSON App. You can start by following the guide on generating SAMSON Extensions. This makes it easier to reuse, distribute, and integrate your tools seamlessly into future projects.
Conclusion
The ability to plug in functionality, avoid redundant coding, and maintain consistency across your workflow is a small shift that can significantly accelerate your modeling projects. SAMSON Apps make this integration process approachable and reusable.
Browse the latest available Apps and get started at the Apps documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.