Molecular modelers often face the challenge of jumping between different tools and platforms to complete different parts of their workflows. Running an optimization in one tool, visualizing it in another, and writing custom scripts to connect them can slow down research productivity and increase the chances of errors or data incompatibility. Fortunately, SAMSON, the integrative molecular design platform, provides a powerful and flexible approach to centralize your tasks through Apps.
SAMSON Apps are lightweight add-ons that bring additional functionality directly into the SAMSON environment. Whether you need to interface with an external executable like AutoDock Vina, wrap existing scientific code, or access web-based services, you can often do it without leaving the interface. Moreover, thanks to the SAMSON API, apps can also introduce completely new capabilities tailored to the needs of computational chemists, structural biologists, and materials scientists.
What can SAMSON Apps do?
Apps can:
- Call external software like AutoDock Vina for docking simulations, directly integrated into SAMSON’s visual environment.
- Wrap your own legacy code or in-house tools—no need to rewrite everything from scratch.
- Communicate with web services, enabling online calculations or database retrieval without a browser.
- Take advantage of the SAMSON API to build entire new user interfaces or algorithms.
Where to find and manage Apps
To find available apps, simply go to Home > Apps within SAMSON. SAMSON comes with a curated set of default apps, but you can expand the platform significantly by connecting to SAMSON Connect. From there, you can explore a rich ecosystem of extensions built by both the SAMSON team and the broader research community.
This makes it easy to configure SAMSON exactly how you need it for your specific research area.
Interested in building your own App?
If you have repetitive workflows or specific tools that you wish were better integrated, SAMSON lets you develop custom apps with your own functionality. Through its Extension Generator and robust documentation, developers can quickly prototype and share their tools with others.
This has the added benefit of helping labs and teams share standardized approaches—reducing setup time for new members and ensuring consistent results.
Example: AutoDock Vina Extended App
The AutoDock Vina Extended App is a great example of what’s possible. Instead of exporting your structure, preparing it with a separate tool, and running docking from a terminal, everything is seamlessly handled within SAMSON. This includes preparing input files, setting parameters, executing the dock, and visualizing results immediately.
Conclusion
By integrating custom and third-party tools into one cohesive interface, SAMSON Apps offer a more streamlined and scalable approach to molecular modeling. Whether you’re building your own pipeline or just looking for a smoother way to work with your favorite tools, SAMSON helps reduce context-switching and improve reproducibility.
You can explore SAMSON Apps and learn more at the official documentation page: https://documentation.samson-connect.net/users/latest/apps/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net