AlphaFold โ How to Interpret Confidence in Predicted Structures
Why this matters
AlphaFoldโs 3D coordinates are model predictions. AF2, AF-Multimer, and AF3 differ in their prediction targets and versions. pLDDT indicates local confidence around each residue, while PAE helps assess uncertainty regarding the relative placement between residues or domains. High confidence does not automatically validate cellular environment, dynamics, alternative states, binding affinity, or biological function. Use predictions as a starting point for mutation design and experimental hypothesis generation, and cross-validate with experimental structures and biochemical/cellular evidence.
Interpretation boundary
This article explains the concept and the limits of the evidence. It does not provide diagnostic, testing, or treatment decisions for an individual patient.