US-align

US-align aligns proteins, RNAs, DNAs, and macromolecular complexes to provide universal structure alignment for monomers and assemblies, enabling comparative analysis and template-based docking across heterogeneous molecular types.

Key Features:

• Universal Alignment Capability: Supports alignment of proteins, RNAs, DNAs, monomer structures, and macromolecular complexes within a unified protocol for heterogeneous oligomer comparison and template-based docking.
• TM-score Objective Function: Employs a uniform TM-score objective function to assess structural similarity across different molecular types.
• Heuristic Alignment Searching Algorithm: Uses a heuristic alignment-searching algorithm that iteratively optimizes the unified objective function to improve alignment speed and precision.
• Benchmark Performance: Demonstrates superior performance in large-scale benchmarks for pairwise and multiple structure alignments across proteins, RNAs, DNAs, and complexes.

Scientific Applications:

• Comparative Structural Analysis: Enables comparison of monomer and complex structures across proteins, RNAs, and DNAs to assess structural conservation and variation.
• Template-Based Docking: Facilitates template-based docking of protein-protein and protein-RNA/DNA complexes for predicting molecular interactions and assemblies.
• Heterogeneous Structure Comparison: Permits fusion and comparison of different molecular types within a single alignment protocol to analyze oligomeric architectures.

Methodology:

Uses a unified TM-score objective function within a unified protocol and a heuristic alignment-searching algorithm that iteratively optimizes the objective function.