For many molecular modelers, one persistent challenge is integrating external tools — whether they’re command-line executables, web services, or in-house scripts — into a unified modeling workflow. Repeatedly shifting data between programs, converting formats, and writing glue code to link everything together can quickly become frustrating and time-consuming.
This is where the concept of apps in SAMSON can make a real difference. SAMSON, the integrative molecular design platform, allows users to extend its functionality through apps — modular extensions that can either connect to external software or provide entirely new features based on the SAMSON API. Whether you’re running molecular docking calculations, analyzing properties, or visualizing data, apps let you plug in tools where they matter most — directly inside your modeling environment.
Here’s how apps can relieve common workflow pain points:
- External connectivity: Have a legacy tool you trust? SAMSON apps can act as connectors, bridging to external executables and web services while shielding you from manual data preparation and conversion.
- Reuse existing code: Instead of rewriting existing Python or C++ functions from scratch, wrap your code into an app and reuse it within SAMSON. This promotes efficiency and reproducibility.
- Custom workflows: Need something specific for your calculations or data prep? SAMSON encourages the creation of custom apps that provide entirely new functionality tailored to your use case.
By default, SAMSON comes with a set of pre-installed apps, but the real power lies in expanding your toolkit via SAMSON Connect, a curated hub where you can browse, install, and manage additional extensions built by the SAMSON community and developers around the world.
One example is the AutoDock Vina Extended App, which integrates the widely used docking software directly into SAMSON. This allows you to run docking simulations without leaving the platform, visualize results natively, and streamline hypothesis testing in drug discovery.
Locating these apps is easy: open the SAMSON interface and find them under Home > Apps. You’ll find a mix of visualization tools, docking engines, dynamics simulations, analysis modules, and more — all designed to work together in the same environment.
If you’re ready to go one step further, consider developing your own apps using the Extension Generator. This documentation walks you through building apps using SAMSON’s rich API and provides templates to get started quickly.
Ultimately, SAMSON’s app ecosystem provides a lightweight, integrated way to turn your favorite tools into seamless components of your modeling workflow — reducing friction while encouraging reuse and modular design.
To explore more about apps in SAMSON, visit the Apps documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.