One of the most common frustrations in biomolecular modeling is the time and effort involved in predicting protein structures. While AlphaFold-2 has become a staple in computational biology due to its impressive accuracy, setting it up and running it locally can be technically demanding and computationally expensive. Enter SAMSON: a platform that makes using AlphaFold-2 in the cloud as straightforward as filling out a form.
If you’re working with proteins and need to quickly obtain high-quality structural models, SAMSON’s Biomolecular Structure Prediction extension can significantly streamline your workflow. Whether you’re preparing models for simulation, visualization, or analysis, the integrated AlphaFold-2 service enables quick, cloud-based predictions—without the need to install or configure AlphaFold yourself.
Why Use AlphaFold-2 in SAMSON?
- Ease of Use: Predict via a straightforward graphical interface—no need to write or debug code.
- Cloud-Based: Computation is done in the cloud, so you can predict on powerful A100 GPU machines without owning the hardware.
- Integrated Workflow: View results directly in SAMSON, with color maps of pLDDT values automatically applied if they’re included in the file.
How the Integration Works
To get started, open Home > Predict in SAMSON, then select AlphaFold-2 from the service list. Paste your FASTA sequence(s), choose your prediction model type (e.g., monomer or multimer), and your preferred database for multiple sequence alignment. After clicking Start prediction, jobs are submitted to the cloud.
The results can be accessed in two ways:
- Inside SAMSON: Interface > Cloud jobs
- On the web: SAMSON Connect > Account > Jobs
Predicted structures are visualized with different colors based on per-residue confidence (pLDDT), helping you quickly assess model reliability.
Managing Cloud Credits
Computations use cloud GPUs and require computing credits. You can either request them by emailing contact@samson-connect.net or purchase them directly from your account.
When to Use It
This feature is ideal if you:
- Need to generate initial models of proteins for docking or molecular dynamics
- Want to validate sequences quickly before investing in wet-lab synthesis
- Collaborate with others and need a reproducible, cloud-based workflow
It is also worth noting that publications arising from work using AlphaFold-2 via SAMSON should cite the original AlphaFold paper and, where applicable, the AlphaFold-Multimer paper.
Learn more about how this works and explore additional structure prediction tools by visiting the SAMSON Biomolecular Structure Prediction documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.