Benchmark of 235 Protein-RNA Complexes for Docking Server Evaluation

235 protein-RNA complexes provide a consolidated benchmark for evaluating template-free docking web servers and AlphaFold Server. The dataset, curated from PDB structures up to July 2024, was used to assess performance metrics like CAPRI success rates. It reveals HDOCK achieved a 44.7% success rate in top 5 predictions, while AlphaFold 3 reached 87.0% overall but showed limitations on complexes outside its training set.

Use Cases

• Compare CAPRI success rates across five template-free docking servers and AlphaFold Server using the 235 benchmark complexes.
• Analyze the 40% success rate of AlphaFold 3 on protein-RNA complexes outside its training set versus docking server performance.
• Identify cases where docking approaches succeeded but AlphaFold 3 failed, using the nine specific instances documented in the benchmark.

Strengths

• Contains 235 curated protein-RNA complexes, providing a substantial benchmark for method comparison.
• Includes performance metrics (e.g., 31.1% and 44.7% success rates for HDOCK) assessed by standardized CAPRI criteria.
• Data is temporally current, sourced from PDB structures deposited up to July 2024.

Limitations

• The dataset is small in file size (301.5 KB), indicating limited scope and potentially summarized results rather than raw structural data.
• Performance analysis is specific to the five evaluated docking servers and AlphaFold Server; results may not generalize to other tools.
• As a benchmark for specific computational methods, its utility is narrow for broader biological discovery without the underlying 3D structures.

Provenance

Source

Curated from Protein Data Bank (PDB) structures.

Collection Method

Compiled into a benchmark dataset for systematic performance assessment of docking servers.

Time Range

PDB structures deposited up to July 2024.

Freshness

Last updated March 2026, based on PDB data current to July 2024.

Geography

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