Viewing 3D Structures

ProtSpace integrates with AlphaFold to display 3D protein structures alongside your embedding visualization.

How It Works

When you select a protein with a UniProt accession:

1. The structure viewer appears in the sidebar below the legend
2. Links to AlphaFold Database, UniProt, and InterPro appear at the top - click them anytime
3. The AlphaFold structure loads automatically via 3D-Beacons API

Supported Structures

Currently, ProtSpace supports AlphaFold structures only. PDB experimental structures are not yet integrated.

Confidence Coloring (pLDDT)

Structures are colored by predicted Local Distance Difference Test (pLDDT) confidence scores—the same scheme used on the AlphaFold Database. Regions in blue are high-confidence, yellow moderate, and red low-confidence. This helps you quickly spot which parts of the model are more reliable.

Viewer Controls

Action	Effect
Left drag	Rotate the structure
Right drag	Pan the view
Scroll	Zoom in/out
Double-click	Reset the view

When Structures Aren't Available

Not all proteins have AlphaFold structures. When no structure is found, the viewer displays:

"No 3D structure was found for <Protein ID>"

Next Steps

• Exporting Results - Save your findings
• FAQ - Common questions