Molecular modelers often struggle to accurately predict biomolecular structures, particularly when working with complex systems or limited experimental data. If you’re one of them, SAMSON’s Biomolecular Structure Prediction extension, with the integration of AlphaFold-2, offers a practical, cloud-based solution for your modeling workflows. Here’s how you can utilize AlphaFold-2 effectively in SAMSON to streamline your structure prediction process.
Why Use AlphaFold-2 in SAMSON?
AlphaFold-2 has set a new benchmark in protein structure prediction, delivering high accuracy. By embedding AlphaFold-2 within SAMSON, you can now accelerate your modeling efforts while leveraging powerful cloud machines, including options with cutting-edge A100 GPUs. This reduces local computing bottlenecks and ensures secure data handling.
The integration within SAMSON makes predictions accessible thanks to a simple and systematic workflow. Here’s everything you need to know to get started.
Step-by-Step Guide
Predicting structures with AlphaFold-2 in SAMSON is straightforward:
- Step 1: Open SAMSON and navigate to
Home > Predict. - Step 2: Select the AlphaFold-2 service from the list of prediction tools.
- Step 3: Upload one or more FASTA files containing your sequences.
- Step 4: Choose an AlphaFold model variant. Options like monomer and multimer cater to different structural setups.
- Step 5: Select a database for multiple sequence alignment, ensuring compatibility with your input data.
- Step 6: Click Start prediction, and let SAMSON handle the rest.
Post-Prediction Workflow
Once the prediction is complete, you can conveniently view the results in SAMSON under Interface > Cloud jobs, or access them directly on SAMSON Connect. Predicted structures are colorized based on pLDDT values (if available), offering insight into model confidence at a glance.
Cost and Computing Resources
AlphaFold-2 calculations are performed using cloud-based machines equipped with A100 GPUs. While this ensures high performance, calculations require computing credits. Computing credits can be purchased on SAMSON Connect. Additionally, SAMSON’s team can guide you on requesting credits to suit your research needs—simply reach out via email.
Citations and Academic Use
If your research includes findings generated using AlphaFold-2 in SAMSON, make sure to cite the respective AlphaFold papers to acknowledge their contributions. Explicit citation instructions can be found in SAMSON’s documentation.
Experience the Benefits
By integrating advanced prediction tools like AlphaFold-2 into your workflow, SAMSON allows you to overcome resource limitations and predict biomolecular structures with ease. This tool is particularly helpful if you are preparing to move your predicted models into downstream applications such as docking or simulations.
Visit the full documentation page at this link to learn more about leveraging SAMSON’s structure prediction features and maximize your modeling capabilities.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.