Setting up and running complex molecular simulations can often require a combination of software tools, each with distinct formats, workflows, or interfaces. For molecular modelers, this fragmentation can become a time sink—slowing down exploration and discovery. If you’ve ever thought, “There must be a simpler way to bring everything together,” then SAMSON Apps might be the solution you’re looking for.
SAMSON Apps are modular tools that seamlessly integrate into SAMSON, the integrative platform for molecular design. These add-ons provide functionality that spans simulation, visualization, analysis, and connectivity to external resources. Instead of juggling multiple standalone tools, molecular modelers can use a centralized environment where everything communicates effortlessly.
What can SAMSON Apps do?
Each SAMSON App adds a specific capability. Some apps act as wrappers, enabling you to use pre-existing tools directly inside the SAMSON environment. Others offer entirely new features built on SAMSON’s architecture. For example:
- Run molecular docking simulations using AutoDock Vina directly inside SAMSON.
- Connect to external web services for structure prediction or property estimation.
- Visualize and manipulate large biomolecular structures interactively.
This modularity means you only install what you need, keeping your workspace focused and efficient.
How to Access Apps
Installed SAMSON Apps can be found easily under Home > Apps in the interface. SAMSON comes with a set of default apps, covering many standard modeling needs. From there, you can visit SAMSON Connect to explore and install more specialized apps developed by the community or the SAMSON team.
This system makes it easy to keep your software up to date with the latest methods, without waiting for large software releases. If a new docking method or visualization technique is made available as a SAMSON App, you can try it out with just a few clicks.
Custom Apps for Custom Needs
If your project requires a tool or workflow that doesn’t yet exist, you can develop your own SAMSON App with the SAMSON Extension Generator. You can wrap legacy code, automate tasks, or create entirely new user interfaces. This opens up possibilities for rapid prototyping and personalized extensions tailored to your daily use cases.
Documentation and developer resources are available in the Documentation center, and the entry point for creating new apps is well-explained, even if you’re new to SAMSON’s API.
Real-World Example: AutoDock Vina Extended App
The AutoDock Vina Extended app integrates trusted molecular docking capabilities into a visual workflow. No need to switch between software packages or convert formats—just import your structures, set your target and ligands, and run the docking directly in SAMSON.
Conclusion
SAMSON Apps streamline your molecular modeling workflows by reducing software fragmentation and enabling a more cohesive user experience. Whether you’re trying to dock a ligand, process protein structures, or visualize molecules more effectively, apps can greatly simplify your process.
To learn more, visit the official documentation page for SAMSON Apps.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.