SymProFold

SymProFold predicts the structure of symmetrical protein assemblies, such as bacterial surface layers and viral capsids, by utilizing AlphaFold-Multimer predictions to test symmetry operations and identify the most likely symmetry for the assembly.

Key Features:

• Symmetry prediction: Tests all known symmetry operations observed in two-dimensional S-layer arrays and spherical viral capsids, including p1, p2, p3, p4, and p6.
• Assembly derivation: Derives symmetrical assemblies from protein sequences using the high accuracy of AlphaFold-Multimer predictions.
• Symmetry identification: Identifies the most likely symmetry for the protein assembly from the tested symmetry operations.
• Experimental validation: Predicted models are validated using available experimental data at the cellular level and additional crystal structures to confirm symmetry and interfaces.

Scientific Applications:

• S-layer structural characterization: Enables structural prediction of cell surface layers that form symmetrical lattices on bacterial and archaeal cells, facilitating cell adhesion, immune system evasion, and environmental stress protection.
• Viral capsid prediction: Predicts spherical viral capsid structures through symmetry-based assembly modeling.
• Nanotechnology and biotechnology: Supports exploration of functionalities and design of targeted applications in nanotechnology, biotechnology, medicine, and materials and environmental sciences.

Methodology:

The pipeline utilizes AlphaFold-Multimer predictions to derive symmetrical assemblies from protein sequences, specifically focusing on two-dimensional S-layer arrays and spherical viral capsids.