Efficient Structure Prediction with AlphaFold-2 in SAMSON

Molecular modelers often face the challenge of predicting biomolecular structures accurately and efficiently. Whether you’re deciphering protein folding, examining multimer interactions, or tackling multisequence alignments, having the right tools is crucial. The Biomolecular Structure Prediction extension in SAMSON provides a powerful solution for such tasks, particularly through its integration with AlphaFold-2.

Why Use AlphaFold-2 in SAMSON?

AlphaFold-2 is one of the most advanced tools available today for predicting protein structures with remarkable accuracy. Within SAMSON, it is seamlessly integrated for easy, step-by-step workflow processing combined with secure cloud-based calculations. This makes it accessible for both beginners and experienced modelers.

Steps to Predict Structures with AlphaFold-2

Using AlphaFold-2 in SAMSON is straightforward and designed for efficiency:

  • Step 1: Navigate to Home > Predict.
  • Step 2: Select the AlphaFold-2 service.
  • Step 3: Upload your sequences via one or more FASTA files.
  • Step 4: Customize your prediction by choosing AlphaFold models (e.g., monomer or multimer) and selecting the appropriate database for multiple sequence alignment.
  • Step 5: Click Start prediction to initiate the computation.

Cloud-Based Efficiency

All calculations are performed on high-performance cloud resources, including options for powerful A100 GPU instances. Not only does this save local resources, but it also ensures faster results. You can monitor your ongoing predictions either directly in SAMSON under Interface > Cloud jobs or on your account at SAMSON Connect > Account > Jobs.

Understanding Your Results

Once your structures are predicted, SAMSON provides intuitive insights to help you analyze your results:

  • Structures are automatically colorized based on pLDDT values (if available), providing a clear visual representation of confidence levels.
  • You can share cloud job results with collaborators directly through SAMSON.
SAMSON structure prediction

Credits and Publishing

It’s important to note that structure predictions use computing credits—something you can purchase directly via SAMSON's credit system, or request by contacting SAMSON support. If your research leads to publications based on AlphaFold-2 predictions, remember to cite the AlphaFold paper, as outlined in the documentation.

Learn More

For detailed guidance and additional features, explore the original SAMSON documentation at this link.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON for free at SAMSON Connect.

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