Protein structure prediction is a critical challenge in molecular modeling. Whether you’re studying a novel enzyme, designing a therapeutic target, or working with systems biology models, knowing the precise structure of a protein is essential—but experimentally determining that structure can take weeks or months.
If you’ve struggled with limited computational resources or complex pipelines to access AlphaFold, there’s now a simpler way. SAMSON, the integrative molecular design platform, offers a streamlined and user-friendly interface for running AlphaFold-2 predictions directly in the cloud.
Why run AlphaFold-2 in SAMSON?
AlphaFold-2 has demonstrated remarkable accuracy in predicting protein structures based on sequences. However, setting up AlphaFold locally can be technically demanding and computationally expensive. With SAMSON, you can run AlphaFold-2 predictions with only a few clicks, using powerful cloud machines (including A100 GPUs) and a simple graphical interface.
Getting started
To run AlphaFold-2 in SAMSON, make sure the Biomolecular Structure Prediction extension is installed. Then:
- Go to
Home > Predictin the SAMSON interface. - Select AlphaFold-2 from the available services.
- Choose the FASTA file(s) corresponding to your protein(s).
- Select the prediction model (e.g., monomer, multimer) and the sequence alignment database.
- Click Start prediction.
What happens behind the scenes?
The prediction task is submitted to the cloud and securely processed. Computing credits are used depending on the performance of the selected cloud machine—higher-end GPUs may cost more but yield faster results.
Viewing results
Once your structure is ready, it will appear in your SAMSON workspace and in the Interface > Cloud jobs panel. SAMSON will automatically colorize predicted structures based on pLDDT scores, helping you visually assess prediction confidence.
You can also access your predictions through SAMSON Connect > Account > Jobs.
What about publications?
If you use results from AlphaFold-2 in your research, be sure to cite the original AlphaFold paper. For multimers, also cite the AlphaFold-Multimer paper where applicable.
Need computing credits?
Contact SAMSON support to request free computing credits or purchase more directly through this page.
Running AlphaFold-2 doesn’t have to be difficult or hardware-intensive. SAMSON makes it easier for researchers to stay focused on science rather than setup.
To learn more about the Biomolecular Structure Prediction extension in SAMSON, visit the official documentation page: https://documentation.samson-connect.net/tutorials/bsp/bsp/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net