Accurate prediction of protein structures is essential in many areas of molecular modeling—from drug design to understanding protein function. However, running AlphaFold-2 locally can be technically demanding and resource-intensive, especially without top-tier GPUs and data setup. For many researchers and students, the barrier to entry is still high.
Fortunately, SAMSON makes it easy to predict protein structures with AlphaFold-2, using a streamlined interface and cloud computation. No need for complicated server setups or downloading large models—just open SAMSON, submit your FASTA files, and let the cloud servers do the work.
Cutting through the complexity
Using AlphaFold-2 in SAMSON is designed to be as intuitive as possible:
- Navigate to Home > Predict.
- Select the AlphaFold-2 service.
- Provide your input through one or more FASTA files.
- Select the prediction model type (e.g., monomer or multimer), and optionally, the alignment database.
- Click Start prediction.
The results are computed in the cloud, so your local machine doesn’t need to have a high-end GPU. Once complete, you can easily view the results in SAMSON under Interface > Cloud jobs or on your SAMSON Connect account.
Interpreting results visually
One of the useful features of SAMSON’s AlphaFold integration is the automatic color-coding of structure confidence. Predicted structures are displayed with coloring based on pLDDT values (Predicted Local Distance Difference Test), where blue typically corresponds to high confidence and red indicates low confidence. This helps users quickly identify which regions of the model are reliable and which may need further investigation.
Cloud computing made simple
Predictions are run on powerful cloud machines equipped with A100 GPUs. This means fast computations without investing in your own infrastructure. Various options exist with different performance levels and costs.
To get started, you can request or purchase computing credits directly from your SAMSON Connect account. For academic users, this often proves more convenient than setting up local AlphaFold pipelines.
Why this matters
AlphaFold-2 predictions embedded in SAMSON open up new possibilities for:
- Rapid structure exploration during early-stage research
- Educational use in classrooms or workshops without technical overhead
- Running multiple models in parallel via the SAMSON interface
If you include predictions in a publication, be sure to cite the original AlphaFold paper and the AlphaFold-Multimer paper, if relevant.
To learn more about this and other biomolecular structure prediction tools in SAMSON, visit the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.