For many molecular modelers, predicting accurate protein structures can be time-consuming or require specialized installations and command-line experience. If you’re exploring protein structure prediction and want a streamlined, interactive experience that works directly within a user-friendly software platform, this post is for you.
SAMSON, the integrative molecular design platform, offers a Biomolecular Structure Prediction extension that integrates powerful services such as AlphaFold-2, directly accessible from the graphical interface. This is particularly useful for those who want fast results and visual feedback without switching between tools.
Why Use AlphaFold-2 in SAMSON?
AlphaFold-2 has rapidly become a standard tool in protein structure prediction, offering high accuracy for a wide range of sequences. It traditionally requires setting up complex environments and scripting workflows, but in SAMSON, predictions can be launched in a few clicks.
How It Works in SAMSON
To start using AlphaFold-2 inside SAMSON:
- Open SAMSON and go to Home > Predict.
- Select AlphaFold-2 as your prediction service.
- Upload one or more sequences in FASTA format.
- Select your preferred AlphaFold model (e.g., monomer, multimer).
- Choose the database for sequence alignment.
- Click Start prediction.
Your prediction will be processed in the cloud using secured data transmission. Depending on your selected model and cloud configuration, computations will be run on powerful hardware, including A100 GPUs. Results typically become available within minutes, depending on sequence length and service load.
Viewing and Interpreting Results
After completion, results can be viewed directly in SAMSON:
- In SAMSON, go to Interface > Cloud jobs.
- Or check online at your SAMSON Connect job dashboard.
Structures are automatically colorized based on their pLDDT confidence values (if available). This allows you to assess which regions of the model are more or less certain—directly within the 3D interface.
About Computing Credits
Each job requires computing credits since predictions run on cloud GPUs. You can request credit allocations or purchase credits depending on your prediction needs.
If your publication involves results from AlphaFold-2 predictions via SAMSON, make sure to cite:
Jumper et al., Nature (2021)
When and Why Use This?
If your research involves sequences with unknown structures or you need to validate folded states before docking or dynamics, this tool is a practical choice. It’s ideal in educational settings too, allowing students to go from sequence to 3D without complex pipelines.
Try It Yourself
Even if you’re just exploring new protein designs or modeling known families with unknown variants, this approach simplifies your workflow. You’re one FASTA file away from a visualized structure.
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.