Predicting accurate protein structures remains one of the most time-consuming steps in molecular modeling and drug discovery. Researchers often struggle with limited local hardware, complex pipelines, and long waiting times using public services. Fortunately, SAMSON offers an integrated and user-friendly solution through its Biomolecular Structure Prediction extension, making it easy to run AlphaFold-2 predictions directly from the interface, in just a few steps.
AlphaFold-2, developed by DeepMind, is known for its breakthrough results in protein structure prediction. It’s widely used in structural biology research, but many workflows require downloading large databases, configuring scripts, and setting up computational environments—especially challenging for non-experts in bioinformatics.
SAMSON simplifies this process by offering cloud-based AlphaFold-2 predictions through a graphical interface. You don’t need a powerful local GPU—predictions are performed on demand using cloud machines, including access to A100 GPUs for faster results.
How It Works in SAMSON
- Open the command path Home > Predict in the SAMSON interface.
- Select the AlphaFold-2 service from the list.
- Submit your input in FASTA format. You can add multiple sequences if needed.
- Choose the desired prediction model (e.g., monomer, multimer) and the database for multiple sequence alignment.
- Click Start prediction to launch your task on the cloud.
What You Get
Once the job is submitted, you can monitor its progress through Interface > Cloud jobs or your SAMSON Connect account under Account > Jobs. When results are loaded back into SAMSON, they are automatically colorized based on pLDDT values, indicating prediction confidence—a visual aid that helps you assess structure quality at a glance.
This workflow is especially useful for researchers who:
- Don’t have access to local high-performance compute infrastructure
- Need to quickly test multiple sequences or variants
- Prefer GUI-based environments over command-line tools
Why It’s Useful
In academic labs or teaching environments, setting up AlphaFold locally can be a deterrent to adoption. SAMSON removes that friction, letting you focus on science instead of systems. You can use AlphaFold-2 directly in the same environment where you model, simulate, or even visualize interactions—cutting down on workflow switching and data transfer.
You can request or purchase computing credits depending on your needs. For more intensive workloads or collaborative projects, this flexibility can accelerate research without requiring infrastructure investments.
Start Quickly
To explore this AlphaFold-2 workflow in SAMSON, visit the official documentation page for detailed step-by-step instructions: https://documentation.samson-connect.net/tutorials/bsp/bsp/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON today at https://www.samson-connect.net.