Molecular modeling often requires researchers to juggle between different tools—running simulations in one software, visualizing results in another, and scripting custom analyses somewhere else. This not only increases the risk of errors during data transfer, but it also wastes valuable time.
One solution to this problem lies in SAMSON’s App architecture. If you’re new to SAMSON or haven’t yet explored its under-the-hood flexibility, SAMSON Apps allow you to bring a wide variety of tools—such as external executables or web services—directly into your modeling workflow.
For example, you could integrate a molecular docking executable like AutoDock Vina, a quantum chemistry library, or even a Python-based analysis script as a SAMSON App. This helps bridge your existing tools and SAMSON’s graphical and scripting environments, all while maintaining a responsive and cohesive modeling interface.
What is a SAMSON App?
A SAMSON App is a software extension that either adds new functionality or acts as a wrapper around external software. The idea is to eliminate workflow siloing: instead of running code separately, you streamline the experience inside SAMSON’s user interface.
Apps may:
- Act as connectors to external tools or services, including command-line and cloud-based software
- Wrap legacy code so it works within SAMSON and alongside other SAMSON Extensions
- Implement new functionality from scratch using the SAMSON API
Why bother wrapping external tools?
Here are some common issues faced by molecular modelers:
- File format incompatibility: Shuffling between tools often ends with tedious format conversions.
- Lack of interactivity: Command-line tools don’t usually offer visual feedback.
- Fragmentation: Complex workflows require multiple interfaces, raising the learning curve.
By wrapping these tools into SAMSON Apps, you centralize your workflow. The model you’re visualizing is the same one being processed, and the results show up right where you want them—in real time, right on your molecules.
How to add apps
SAMSON provides a core set of default Apps when you first install it. You can then extend this functionality by visiting the in-app Apps section under Home > Apps, or browsing SAMSON Connect to add more extensions as needed.
The good news is: you don’t need to reinvent the wheel. For many common use cases—such as docking, molecular dynamics, or electrostatic analysis—you’ll find ready-made Apps, saving you time and effort.
Want to build your own?
If you’re a developer or researcher who already uses specialized tools, you can also build your own App using the Extension Generator. The generator kickstarts your development by scaffolding key files based on your selected functionality (visual model, simulator, interaction model, etc.).
Extensive resources are available in SAMSON’s Extension Generator documentation and the Documentation center.
By integrating your preferred tools into one workspace, SAMSON helps reduce errors, accelerate discovery, and improve reproducibility.
To learn more, head over to the official Apps documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.