One of the challenges molecular modelers face is predicting accurate biomolecular structures, especially for proteins that lack experimental structures. With the Biomolecular Structure Prediction extension in SAMSON, the process of leveraging advanced prediction tools like AlphaFold-2 becomes seamless and highly accessible.
Why Use AlphaFold-2 in SAMSON?
AlphaFold-2 is an advanced tool for protein structure prediction, applauded for its accuracy. Integrating this capability into SAMSON lets modelers harness its potential directly within a molecular design platform, eliminating the need for separate setups or extensive computing hardware. SAMSON sends data via secure connections to cloud computing services, enabling high-performance structure prediction even from low-spec machines.
A Step-by-Step Guide
Launching structure predictions with AlphaFold-2 in SAMSON is straightforward:
- Navigate to Home > Predict in SAMSON.
- Select the AlphaFold-2 service.
- Upload one or more FASTA files containing your protein sequences.
- Choose the appropriate AlphaFold model (e.g., monomer, multimer) and select the database for multiple sequence alignment.
- Click Start prediction to initiate the process.
What Happens Next?
Once the prediction starts, calculations are performed using a range of powerful cloud machines, including options with A100 GPUs for faster processing. The results are accessible within SAMSON under Interface > Cloud jobs or on SAMSON Connect > Account > Jobs.
An additional feature modelers will appreciate is that when the results are loaded back into SAMSON, structures are color-coded by pLDDT values (if available). This helps immediately identify regions of higher and lower prediction confidence, guiding further modeling decisions.
Credits and Publishing
Running an AlphaFold-2 prediction uses computing credits. To request or buy credits, you can contact SAMSON or purchase computing credits here.
If your research involves findings from AlphaFold-2 predictions, make sure to cite the AlphaFold paper and, if applicable, the AlphaFold-Multimer paper in your publication.
Why It Matters
With its integration in SAMSON, AlphaFold-2 transitions from being a cutting-edge technology to a user-friendly tool accessible to experts and beginners alike. Modelers no longer need to worry about accessing high-end GPUs or dealing with complex setups. SAMSON simplifies the workflow while ensuring secure data handling and high-quality outputs.
To dive deeper into predicting biomolecular structures with AlphaFold-2 using SAMSON, check out the detailed documentation here.
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