For many molecular modelers, one of the biggest obstacles with software platforms is integrating external tools or custom algorithms into their workflow. Often, powerful algorithms or scripts are developed in separate environments, making it difficult to combine them with visualization, analysis, or simulation tools. This leads to fragmented workflows, extra time spent converting file formats or switching interfaces, and ultimately limits productivity.
SAMSON, the integrative molecular design platform, provides a solution to this problem with its modular architecture that supports the integration of external tools through Apps. An App in SAMSON can serve a wide range of purposes: it might interact with an external executable or web service, wrap code that was developed independently, or introduce entirely new functionality via the SAMSON API.
This flexibility allows you to bring your preferred methods and tools directly into the SAMSON environment, and combine them with the platform’s own features or other SAMSON Extensions. Whether you’re working on molecular docking, quantum computations, machine learning models, or anything else—Apps let you centralize and streamline your work.
For example, the AutoDock Vina Extended App integrates molecular docking capabilities directly in SAMSON, letting users prepare ligands and proteins, perform docking, and analyze results in a single interface:
But what if you want to build your own App?
Getting started is simpler than you might expect. SAMSON provides comprehensive documentation about generating Extensions that can include Apps. You can start by following the guide on generating SAMSON Extensions, which walks you through setting up an Extension—even if what you’re building is just intended to wrap a script or executable you already use internally.
When your App is ready, SAMSON’s ecosystem supports distribution and sharing with collaborators via SAMSON Connect. You can keep your App private or publish it for others, depending on your needs.
Apps are accessible within the SAMSON interface under Home > Apps. SAMSON includes several Apps by default, and more can be added at any time from SAMSON Connect.
This modular approach helps researchers maintain an integrated workflow and avoid platform-hopping. Whether you’re adapting existing tools or designing new computational approaches, Apps offer a clean path toward deeper integration and higher efficiency.
Learn more about Apps in SAMSON and how to develop your own by visiting the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download the platform at https://www.samson-connect.net.