Arena

Arena reconstructs full-atomic RNA structures from coarse-grained models to produce complete, clash-free models suitable for structural analysis.

Key Features:

• Full-Atomic Reconstruction: Reconstructs RNA structures at atomic resolution from inputs with minimal atomic information, including models containing only a single phosphorus atom per nucleotide.
• Iterative Refinement Process: Uses an iterative refinement algorithm to place missing atoms and optimize their positions to minimize nonideal geometries and steric clashes.
• High Accuracy and Speed: Delivers an average RMSD of 3.63 Å to experimental structures while substantially reducing structural clashes.
• Benchmarking Success: On a benchmark of 361 RNA structures, outperformed PDBFixer and C2A with up to 353× faster runtimes and 46× greater efficiency, completing reconstructions in under three seconds per structure.

Scientific Applications:

• Structural Biology Research: Provides full-atomic RNA models for analyses of folding, structure, and interactions with proteins or small molecules.
• Drug Design and Development: Generates atomic-resolution RNA models to support molecular docking and rational design of small molecules targeting RNA.
• Educational Purposes: Supports teaching of RNA structure prediction and refinement methodologies.

Methodology:

Identifies missing atoms in coarse-grained models and iteratively places and refines atom positions to optimize geometry and eliminate steric clashes.