One challenge many molecular modelers face is bridging the gap between specialized external tools and their main modeling platform. Whether it’s docking software, simulation packages, or web-based services, integrating these into a single workflow often means jumping through file conversions, scripting workarounds, or juggling user interfaces.
This is where SAMSON’s Apps offer a flexible solution. Instead of forcing users into a rigid environment, SAMSON Apps provide a way to bridge the gap between SAMSON and a wide range of external executables, web services, and custom-developed code. This allows researchers to keep using their preferred tools while leveraging the connectivity and visualization power of SAMSON.
What is a SAMSON App?
In SAMSON, an App is a type of Extension that can add a broad range of functionality. It’s not limited to graphical interfaces or small plugins – an App might:
- Act as a connector to an external executable tool
- Implement communication bridges to remote web services
- Wrap previously developed code (e.g. analysis scripts, computational tools)
- Provide standalone features built directly using SAMSON’s API
This flexibility is especially valuable for researchers who already rely on robust tools like AutoDock Vina for docking or GROMACS for molecular dynamics. Instead of switching back and forth between software, they can integrate these tools directly through Apps – either existing ones or custom-built.
Where to Find Apps
Apps are accessible from the SAMSON interface, under Home > Apps. By default, SAMSON includes a selection of apps to get you started. But the real power comes from SAMSON Connect, where you can browse and download more Apps contributed by other users and developers.
Want to Develop Your Own App?
For researchers with coding experience, developing your own App is a way to seamlessly bring your computational tools into the SAMSON ecosystem. The Extension Generator makes it easier to get started, and comprehensive documentation is available in the Documentation Center.
For example, if you have a command-line tool that analyzes molecular trajectories, you could develop a SAMSON App that calls your executable behind the scenes, processes its outputs, and displays the results interactively in SAMSON. This turns a fragmented workflow into a smooth, unified experience.
Conclusion
Simplifying tool integration is about enabling more focused research and less time spent managing file formats, interfaces, and intermediate steps. SAMSON Apps make it possible to bring all the pieces of your computational molecular modeling pipeline into one place.
If you’re interested in exploring further or building your own App, check out the full documentation on the SAMSON Apps documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download it at https://www.samson-connect.net.