Predicting a protein’s 3D structure has often been a time-consuming step for molecular modelers. For many, setting up command-line environments, ensuring accurate input formatting, and managing computational resources can slow down early-stage research. If you’re looking for a more streamlined way to predict structures, there’s a practical tool worth exploring: SAMSON’s AlphaFold-2 integration.
SAMSON, the molecular design platform, integrates AlphaFold-2 through its Biomolecular Structure Prediction extension. It allows researchers to submit sequences to the AlphaFold-2 model through an intuitive graphical interface—no complex environment setup required. Below, we explore how this feature addresses a recurring pain point in structural modeling: efficient and accessible structure prediction.
What can you expect?
Using AlphaFold-2 via SAMSON lets you:
- Submit one or more FASTA files
- Select AlphaFold model types (e.g., monomer or multimer)
- Choose the appropriate multiple sequence alignment (MSA) database
- Run predictions on the cloud using high-performance A100 GPUs
Once the prediction is complete, the 3D structure is automatically colorized based on pLDDT confidence scores. This helps you rapidly assess result reliability without needing to interpret raw data manually.
How to Begin a Prediction
- Open SAMSON and go to Home > Predict.
- Choose AlphaFold-2 from the available services.
- Upload one or more FASTA files containing your sequence(s).
- Select the appropriate model and MSA database depending on your target.
- Click Start prediction.
SAMSON processes predictions via cloud machines. You can monitor progress in Interface > Cloud jobs or directly through your SAMSON Connect account under Account > Jobs.
Tip: Predictions run on different clusters, including powerful A100 GPU cloud instances. Resources are accessed using computing credits that can be purchased or requested by contacting the SAMSON team.
Why This Matters
Many researchers spend valuable hours each week wrestling with bioinformatics pipelines just to get a preliminary structure. By lowering the entry barrier, SAMSON helps shift time from infrastructure management toward scientific analysis and design. This is especially helpful in multidisciplinary teams where not all members are computational experts.
Moreover, the automatic coloring of resulting models by pLDDT lets collaborators quickly evaluate confidence levels, making collaboration more efficient.
A Few Things to Keep in Mind
- If your results will be published, remember to cite the relevant AlphaFold papers listed in the documentation.
- Large jobs may require additional computing credits, so plan accordingly if you’re working on high-throughput projects.
Wrapping Up
SAMSON’s GUI integration of AlphaFold-2 offers researchers a reliable and efficient entry point into structure prediction. Whether you’re validating a novel target or preparing input for docking simulations, this workflow saves time and encourages data-driven iterations in molecular design.
To learn more and explore all features of the Biomolecular Structure Prediction extension, visit the full documentation: 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.