What is pLDDT? Reading AlphaFold Confidence Scores Before Docking

By BioDockify Computational Research Team · September 19, 2026 · Guide

pLDDT explained: thresholds (90/70/50), PAE matrices, why AlphaFold hallucinates loops, and exactly which residues to trust or delete before molecular docking.

Read the complete article with tables, code and references on BioDockify.

Key References

• Mariani, V. et al. lDDT: a local superposition-free score for comparing protein structures. Bioinformatics 29, 2722–2728 (2013). DOI: 10.1093/bioinformatics/btt473
• Tunyasuvunakool, K. et al. Highly accurate protein structure prediction for the human proteome. Nature 596, 590–596 (2021). DOI: 10.1038/s41586-021-03828-1
• EMBL-EBI Training. pLDDT: Understanding local confidence. https://www.ebi.ac.uk/training/online/courses/alphafold/
• Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493–500 (2024). DOI: 10.1038/s41586-024-07487-w
• AlphaFold Protein Structure Database FAQ. https://alphafold.ebi.ac.uk/faq

Scope & Limitations

pLDDT measures agreement with the model's own ensemble, not truth — a confidently wrong fold still colors blue High pLDDT does not validate side-chain rotamers at docking-relevant precision PAE is only informative between domains; it says nothing about local loop geometry