Whether you are docking ligands, visualizing interactions, or performing more advanced simulations, chances are you’ve repeatedly jumped between tools that don’t quite integrate well. This friction can cost not only time but also accuracy, especially when transferring data or redoing steps to match software constraints. For molecular modelers looking for smoother workflows, SAMSON Apps offer a practical solution.
SAMSON, the integrative molecular design platform, includes an Apps system that allows you to customize your modeling environment and extend it with specialized features. Instead of bolting on external software manually, SAMSON Apps let you bring versatile functions right into your interface — whether it’s to automate tasks, extend your visualizations, or integrate with web services.
What is a SAMSON App?
An app in SAMSON is a packaged extension that can provide any kind of functionality you need for molecular design. That includes connecting to third-party tools like docking engines, or even running custom scientific pipelines developed completely in-house. Apps can be simple wrappers for automating frequently performed calculations or sophisticated integrations that turn SAMSON into a full platform for interactive simulations or analysis.
For example, the AutoDock Vina Extended App is an app available in SAMSON that greatly simplifies molecular docking workflows by providing a built-in interface to the docking engine. Here’s a look at it:
Why does this matter?
Many workflows in computational chemistry and molecular modeling require repeated interaction with different specialized tools: docking engines, force-field generators, trajectory analyzers, etc. Setting up pipelines involving these tools usually requires scripting and manual file conversion, increasing the likelihood of errors.
With SAMSON Apps:
- You can eliminate most file conversions — many apps are natively compatible with your models inside SAMSON.
- You can use visual interfaces — no command line input is needed once the app is configured.
- You can extend your modeling environment — add only the features you need from SAMSON Connect.
- You can build your own app if your workflow is unique — more on this below.
Where to start?
Apps included by default in SAMSON are accessible from the interface via Home > Apps. You can find and install additional apps directly from SAMSON Connect. The app ecosystem includes options for docking, molecular dynamics, visual analytics, and scripting interfaces, among others. If a particular workflow you need is missing, there’s a well-documented pathway to creating your own extension thanks to the Extension Generator.
Should you develop your own app?
If you’re repeatedly writing scripts to process or analyze molecules in a particular way, then yes — writing your own SAMSON extension might be useful. Apps provide a way to embed your logic directly inside the modeling environment, saving you the trouble of reshaping input data or exporting intermediate results.
Whether you’re integrating a custom scoring function, linking to a remote database, or building new interactive visuals, SAMSON’s API gives you the infrastructure needed to bring it all together.
Conclusion
The ability to add specific tools and even build your own opens the door to a more streamlined way of working. For molecular modelers seeking flexibility without leaving the modeling environment, Apps in SAMSON are an intuitive and powerful option. To explore more or view the list of available apps, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.