Protein structure prediction is often a critical step for molecular modelers, but it can be a tedious process requiring specialized tools and resources. The AlphaFold-2 integration in the Biomolecular Structure Prediction extension for SAMSON makes it straightforward to predict biomolecular structures with high accuracy, all in just a few steps.
Why AlphaFold-2?
AlphaFold-2 represents a breakthrough in protein structure prediction, offering highly accurate results based on DeepMind’s powerful AI. However, molecular modelers often face barriers in accessing AlphaFold-2 due to infrastructure limitations, data format complexities, or resource requirements. SAMSON eliminates these hurdles by allowing you to run AlphaFold-2 predictions via cloud-based resources directly from the platform, saving time and enabling results tailored to your specific modeling needs.
How to Use AlphaFold-2 in SAMSON
Here’s how you can start predicting protein structures with AlphaFold-2 in SAMSON:
- Navigate to Home > Predict in the SAMSON interface.
- Select the AlphaFold-2 service from the available options.
- Provide one or more FASTA files containing the sequences you want to predict.
- Customize your prediction by choosing the AlphaFold model suitable for your needs (e.g., monomer or multimer) and by selecting a database for multiple sequence alignment.
- With your parameters set, click Start prediction. Simple and efficient!
Effortless Visualization and Analysis in SAMSON
Once the prediction is complete, results are seamlessly integrated into your SAMSON environment. Structures with pLDDT scores (a confidence metric provided by AlphaFold) are colorized automatically, enabling you to immediately assess areas of high and low confidence. Access results through Interface > Cloud jobs or on SAMSON Connect, giving you flexibility in managing and analyzing your data.
Cost-Effective and Scalable Cloud Resources
Predictions in SAMSON are powered by advanced cloud computing technologies. Choose from a range of machines, including options equipped with powerful A100 GPUs, to match your requirements and budget. Whether you’re a researcher handling complex structures or a beginner exploring protein modeling, you can find the right resource for your needs. For convenience, you can purchase computing credits here, or contact the SAMSON team to inquire about additional credits.
Citing AlphaFold in Publications
Studies using AlphaFold results should properly acknowledge the original research by citing the AlphaFold paper and, if applicable, its multimer model. This maintains alignment with academic and research standards while sharing your discoveries.
Learn More
Whether you’re new to AlphaFold-2 or looking to enhance your computational toolkit, SAMSON’s integration makes biomolecular structure prediction simpler and more accessible. You can explore further details by visiting the complete documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.