Bridging prediction and reality: Comprehensive analysis of experimental and AlphaFold 2 full-length nuclear receptor structures.

ABSTRACT: AlphaFold 2 has revolutionized protein structure prediction, yet systematic evaluations of its performance against experimental structures for specific protein families remain limited. Here we present the first comprehensive analysis comparing AlphaFold 2-predicted and experimental nuclear receptor structures, examining root-mean-square deviations, secondary structure elements, domain organization, and ligand-binding pocket geometry. While AlphaFold2 achieves high accuracy in predicting stable conformations with proper stereochemistry, it shows limitations in capturing the full spectrum of biologically relevant states, particularly in flexible regions and ligand-binding pockets. Statistical analysis reveals significant domain-specific variations, with ligand-binding domains showing higher

SUBMITTER: Mazhibiyeva A 

PROVIDER: S-EPMC12149446 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature