Predicting the 3D structure of proteins used to require extensive computational setups and technical expertise. For many molecular modelers, integrating AlphaFold-2 into their workflow means either accessing a command-line toolchain or relying on third-party web services — both of which can introduce delays, limitations, or inconsistencies.
With SAMSON’s Biomolecular Structure Prediction extension, it’s now possible to access AlphaFold-2 predictions directly through a visual interface, with cloud computing support and just a few clicks.
Why integrate AlphaFold-2 with SAMSON?
AlphaFold-2 is one of the most widely recognized tools for protein structure prediction. However, its installation and use can be complex or require access to powerful infrastructure. SAMSON simplifies this by offering a graphical interface and automated cloud submission while giving users control over model types and fast data visualization. Here’s how you can work with AlphaFold-2 in SAMSON.
Step-by-step prediction
- Launch the Biomolecular Structure Prediction extension via
Home > Predict. - Select the AlphaFold-2 service.
- Enter one or several protein sequences using FASTA files.
- Choose your desired AlphaFold-2 model (e.g., monomer or multimer models).
- Select a database for multiple sequence alignment (MSA).
- Click Start prediction to send the job to the cloud.
Once submitted, your predictions will be processed using high-performance cloud machines, including access to powerful A100 GPUs. SAMSON lets you monitor the job status directly within the platform through Interface > Cloud jobs or by logging into your SAMSON Connect account.
Viewing your results
After prediction, the resulting structures are loaded automatically into the SAMSON workspace. If pLDDT scores are available, SAMSON will automatically colorize your protein models to reflect local confidence across the structure, helping you assess which regions are reliable at a glance.
This rapid feedback loop eliminates the need to export, convert, or interpret multiple flat files from external services — everything is visual and integrated.
Credits and computing
AlphaFold-2 predictions in SAMSON are paid with computing credits. Prediction costs depend on the selected model and input complexity. If you’re part of an academic or research group, you can contact the team to request computing credits, or purchase credits directly via the SAMSON computing credits portal.
Benefits for molecular modelers
Using AlphaFold-2 in SAMSON simplifies structure prediction pipelines in several ways:
- No need for local AlphaFold installations or set-ups
- No scripting required — everything happens via clicks
- Direct visualization of results and confidence metrics
- Cloud-based computing with GPU acceleration
By merging cloud prediction and local visualization into a single workflow, SAMSON reduces friction when working with AlphaFold-2 and frees time to focus on downstream modeling, simulations or analysis.
To learn more about using AlphaFold-2 in SAMSON, read the full documentation here: 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.