pLDDT Values in AlphaFold2 Protein Models Are Unrelated to Globular Protein Local Flexibility

Abstract

Two non-redundant, high-quality sets of protein X-ray crystal structures from the Protein Data Bank (room temperature, 288–298 K, and low temperature, 95–105 K) were compared to structural predictions conducted using ColabFold/AlphaFold2. In particular, the relationship between B-factors and pLDDT values, which estimate the degree of prediction confidence, was investigated. It was observed that there is basically no correlation between these two quantities and, consequently, that the level of confidence in predictions does not provide information about the degree of local structural flexibility of globular proteins.

Keywords

• AlphaFold
• B-factor
• ColabFold
• pLDDT
• protein data bank