RPXDock

RPXDock performs sequence-independent rigid-body protein docking to design and assemble multi-subunit structures with point group and lattice symmetries.

Key Features:

• Sequence-Independence: Operates without reliance on amino-acid sequence, enabling docking of cyclic oligomers into architectures defined by point group or lattice symmetries.
• Hierarchical Search Algorithm: Employs an efficient hierarchical search strategy to navigate the extensive multidimensional rigid-body docking space.
• Residue-Pair Transform (RPX) Scoring Method: Uses the residue-pair transform (RPX) scoring method to evaluate candidate interfaces based on residue-pair geometries.
• Modular Design: Provides a modular codebase that enables customization and extension for novel symmetric architectures.

Scientific Applications:

• Multi-subunit assembly design: Computational design of multi-subunit protein assemblies across diverse symmetric architectures.
• Vaccine development: Supports computational workflows relevant to vaccine development by enabling arrangement of antigenic subunits in defined symmetric assemblies.
• Nanomaterials design: Facilitates design of protein-based nanomaterials by enabling predictable assembly of building blocks into point group or lattice symmetries.

Methodology:

Combines a hierarchical search approach with the residue-pair transform (RPX) scoring method to explore and filter candidate rigid-body docking configurations within point group and lattice symmetric architectures.