Making the Most of AlphaFold-2 in SAMSON

For molecular modelers, predicting biomolecular structures accurately and efficiently can be a major challenge. With the AlphaFold-2 service in SAMSON, you can predict structures with high accuracy, utilizing cloud-based tools that integrate seamlessly within the platform. Whether you’re working on a single protein or exploring complex multimers, SAMSON’s approach simplifies this essential task.

Streamlined Prediction Workflow

Using AlphaFold-2 in SAMSON is straightforward and involves just a few steps:

  • Navigate to Home > Predict in the SAMSON interface.
  • Select the AlphaFold-2 service.
  • Input your FASTA files—this can include one or multiple sequences.
  • Choose the appropriate AlphaFold model based on your requirements, such as monomer or multimer, and select a database for multiple sequence alignment.
  • Click Start prediction and monitor the progress in the cloud.

From this simple flow, users can gain reliable results that are both secure and well-structured, as the processed data is transferred via a secure connection.

Understanding and Visualizing Results

Once the predictions are complete, AlphaFold-2 will provide structural models that you can analyze directly in SAMSON. The platform adds valuable insights by colorizing structures according to pLDDT values—a prediction metric that indicates confidence levels for different parts of the protein structure.

To view your results:

  • Check Interface > Cloud jobs in SAMSON’s interface.
  • Alternatively, access them on the SAMSON Connect website under Account > Jobs.

This flexibility allows you to choose the most convenient way to review and organize data, depending on your workflow.

Efficient Cloud Computing

AlphaFold-2 calculations in SAMSON take advantage of powerful cloud computing resources. Depending on the complexity of your prediction, SAMSON deploys high-performance cloud machines—many of which are equipped with state-of-the-art A100 GPUs for optimal speed and accuracy.

For those concerned about costs, SAMSON uses a credit-based system for cloud computation. Users can either request credits directly or purchase them online. This system ensures flexibility and scalability, whether you’re conducting occasional predictions or high-throughput analysis.

Pro Tip

Make sure to correctly choose the AlphaFold model and database for the alignment that best mirrors your system. Additionally, remember to cite the AlphaFold and AlphaFold-Multimer papers in any publication that uses findings arising from this service. Proper attribution not only credits the developers but also enhances reproducibility.

Learn More

This guide highlights core features that make AlphaFold-2 predictions in SAMSON intuitive and reliable. Allocating time to explore these features can significantly boost your efficiency in biomolecular modeling. To dive into all details, please read the full Biomolecular Structure Prediction extension documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON today at https://www.samson-connect.net.

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