Protein structure prediction has become an essential tool for researchers in fields ranging from drug discovery to structural biology. If you’ve been relying on standalone tools or web services for structure prediction, switching contexts, managing complex dependencies, and monitoring jobs can be cumbersome. Fortunately, SAMSON’s Biomolecular Structure Prediction extension now makes it possible to predict protein structures using AlphaFold-2—right within the SAMSON environment.
AlphaFold-2 is known for its high-quality predictions, but integrating it into research pipelines has often required some technical know-how. With SAMSON, the process becomes more streamlined and accessible. Here’s an overview of how you can use AlphaFold-2 within SAMSON and why this integration might simplify your structural modeling workflow.
Why Predict in SAMSON?
SAMSON provides a unified interface where prediction, visualization, and analysis can all happen in one place. You don’t need to export sequences, manually submit them to external servers, or wait for emails with download links. Everything—from job submission to result visualization—happens within the platform.
How to Run AlphaFold-2 Predictions in SAMSON
The steps to run a prediction are straightforward:
- Go to Home > Predict in the SAMSON interface.
- Select AlphaFold-2 as your prediction service.
- Upload your FASTA sequences (single or multiple).
- Choose the AlphaFold model type—monomer, multimer, etc.—as well as the sequence alignment database.
- Click Start prediction.
Once your prediction is in progress, you can monitor the job directly in Interface > Cloud jobs or on SAMSON Connect > Account > Jobs. Results are automatically integrated into your workspace when completed.
Understanding the Output
When a result is loaded back into SAMSON, the predicted structure is colorized based on pLDDT values—a measure of confidence for each residue. This helps researchers rapidly assess which regions of the model are more reliable. No additional processing is required to visualize these scores.
Note: AlphaFold predictions in SAMSON are performed on cloud machines, including high-performance A100 GPU instances. This ensures efficient turnaround times even for complex systems. Predictions use computing credits, which can be purchased or requested for evaluation.
When to Use AlphaFold in SAMSON
The integrated approach is ideal if you:
- Need to iterate quickly on structural hypotheses.
- Prefer working within a unified molecular design platform.
- Want real-time visualization of prediction results without manual setup or file transfers.
If collaboration is part of your workflow, SAMSON also makes it easy to share job results and models with colleagues through built-in sharing features.
Conclusion
Integrating AlphaFold-2 with SAMSON could help you save time, reduce overhead, and focus on analysis rather than operations. Whether you’re exploring new targets or validating experimental data, having prediction services accessible within your design environment can make a real difference.
To learn more about biomolecular structure prediction in SAMSON, visit the full documentation at https://documentation.samson-connect.net/tutorials/bsp/bsp/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.